PCN 5160

ISBN 978-1-932946-19-2
A Muslim Archipelago: 

Islam and Politics in Southeast Asia

Max L. Gross

National Defense Intelligence College

Washington, DC

March 2007

The views expressed in this book are those of the author 

and do not refl ect the offi cial policy or position of the 

Department of Defense, the Defense Intelligence Agency, 

or any other agency of the U.S. Government

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Strategic Intelligenc

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The National Defense Intelligence College supports and encourages 

research on intelligence issues that distills lessons and improves Intelligence 

Community capabilities for policy-level and operational consumers.

This book has been many years in the making, as the author explains in his Preface, 

though he wrote most of the actual text during his year as senior Research Fellow with 

the Center for Strategic Intelligence Research. The author was for many years Dean 

of the School of Intelligence Studies at the Joint Military Intelligence College. Even 

though it may appear that the book could have been written by any good historian or 

Southeast Asia regional specialist, this work is illuminated by the author’s more than 

three decades of service within the national Intelligence Community. His regional 

expertise often has been applied to special assessments for the Community. With 

a knowledge of Islam unparalleled among his peers and an unquenchable thirst for 

determining how the goals of this religion might play out in areas far from the focus of 

most policymakers’ current attention, the author has made the most of this opportunity 

to acquaint the Intelligence Community and a broader readership with a strategic 

appreciation of a region in the throes of reconciling secular and religious forces. 

This publication has been approved for unrestricted distribution by the Offi ce of 

Security Review, Department of Defense.

William.Spracher@dia.mil, Editor

Center for Strategic Intelligence Research 

ISBN 978-1-932946-19-2

Library of Congress Control Number 2006937784
iii

CONTENTS

Foreword . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v

Commentary

Allen L. Keiswetter . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

Roger E. Biesel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix

Author’s Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii

Chapter

1. Islam in Southeast Asia: Historical Background . . . . . . . . . . . . . . . . 1

General Considerations . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Historical Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Enter the Europeans . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

The Formation of Malaysia . . . . . . . . . . . . . . . . . . . . . . . 11

The Formation of Indonesia . . . . . . . . . . . . . . . . . . . . . . . 19

2. Islam in Malaysia . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Establishment of Malay Hegemony . . . . . . . . . . . . . . . . . . . 31

Growth of the Islamic Movement . . . . . . . . . . . . . . . . . . . . 34

Mahathir Goes Islamic . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Impact of the Asian Financial Crisis . . . . . . . . . . . . . . . . . . . 42

Militant Islam in Malaysia . . . . . . . . . . . . . . . . . . . . . . . . 45

Impact of the 9/11 Attacks in Malaysia . . . . . . . . . . . . . . . . . 54

Outlook. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

3. Islam in Thailand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

The Sultanate of Patani. . . . . . . . . . . . . . . . . . . . . . . . . . 59

Patani Under Thai Rule . . . . . . . . . . . . . . . . . . . . . . . . . 60

Under the Thai Revolutionary Regime. . . . . . . . . . . . . . . . . . 63

The Pattani Insurgency. . . . . . . . . . . . . . . . . . . . . . . . . . 68

From Nationalism to Islam. . . . . . . . . . . . . . . . . . . . . . . . 73

Revival of the Insurgency . . . . . . . . . . . . . . . . . . . . . . . . 75

Outlook. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

4. Islam in Indonesia. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

Formation of the State Insurgency . . . . . . . . . . . . . . . . . . . . 86

The Islamic Alternative . . . . . . . . . . . . . . . . . . . . . . . . . 86

Fall of Sukarno . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

Ascendancy of the “New Order”. . . . . . . . . . . . . . . . . . . . . 89

Survival of the Revival of Darul Islam . . . . . . . . . . . . . . . . . 95

Formal Establishment of Jemaah Islamiyah . . . . . . . . . . . . . . 102

Fall of the Suharto Regime. . . . . . . . . . . . . . . . . . . . . . . 108
iv

5. Separatism: Threat to Indonesian Unity? . . . . . . . . . . . . . . . . . . 117

East Timor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118

Maluku and Laskar Jihad . . . . . . . . . . . . . . . . . . . . . . . 123

Sulawesi and Jemaah Islamiyah . . . . . . . . . . . . . . . . . . . . 130

Papua . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141

Aceh and GAM . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151

Outlook. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168

6. Islam in the Contemporary Philippines . . . . . . . . . . . . . . . . . . . 171

The Philippines Under American Rule. . . . . . . . . . . . . . . . . 172

The Moros Under Philippine Rule . . . . . . . . . . . . . . . . . . . 178

The Moro Revolt . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183

Split in the MNLF . . . . . . . . . . . . . . . . . . . . . . . . . . . 194

The Post-Marcos Era. . . . . . . . . . . . . . . . . . . . . . . . . . 199

Emergence of Abu Sayyaf . . . . . . . . . . . . . . . . . . . . . . . 202

Ramos and the Moro Problem . . . . . . . . . . . . . . . . . . . . . 205

The Different Approach of Joseph Estrada . . . . . . . . . . . . . . 213

Arroyo Restores the Ramos Policy . . . . . . . . . . . . . . . . . . 215

Outlook. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229

7. Islam and Politics in Southeast Asia . . . . . . . . . . . . . . . . . . . . 233

The First Islamic State . . . . . . . . . . . . . . . . . . . . . . . . . 233

Spread of Islam to Southeast Asia . . . . . . . . . . . . . . . . . . . 236

Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245

Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267
v

Commentary

FOREWORD

Southeast Asia continues to beckon policymakers and scholars alike to revisit its 

history in spite of the tomes of appraisals already written, deconstructive or otherwise. 

Because of a signifi cant presence of Muslims in the region, and particularly in the 

wake of 9/11, it invariably attracts the attention of foreign powers drawn by the specter 

of terrorism and focused on rooting out radical Islamist groups said to be working with 

al-Qa’eda. 

Dr. Max Gross has written an impressive account of the role of Islam in the politics 

of Southeast Asia, anchored by a strong historical perspective and a comprehensive 

treatment of current affairs. The result is very much a post-9/11 book. The origins 

of Jemaah Islamiyah and its connections with al-Qa’eda are carefully detailed. Yet, 

unlike much of the post-9/11 analysis of the Muslim world, Dr. Gross’s research has 

been successful in placing the phenomenon of terrorism within a larger perspective. 

While recognizing that al-Qa’eda’s infl uence on regional terror networks remains 

unclear, it behooves us to be reminded that, regardless of the nature and extent of the 

linkages, to dismiss terrorism as a serious threat to security would be naïve to the point 

of recklessness.

The Muslim Archipelago is a profoundly Islamic region, and Jemaah Islamiyah is 

only a small portion of this reality. The attention Dr. Gross pays to ABIM in Malaysia, 

of which I was a part, and the civil Islam movement in Indonesia, of which the late 

Nurcholish Madjid was a principal spokesman, is greatly appreciated. Those unfamiliar 

with the background and role of the traditional Islamic PAS party in Malaysia, as 

well as the Darul Islam movement in Indonesia, will fi nd the author’s account highly 

benefi cial. The MNLF, the MILF, and Abu Sayyaf in the Philippines, as well as the 

various Islamic movements in southern Thailand, are also carefully explained. 

As a retired career employee of the U.S. Department of Defense, Dr. Gross has paid 

much attention to security issues, highlighting the confl icts that continue to beset us 

and efforts by the governments of the region to resolve them even as fi nal settlements 

remain elusive. In the discourse of the impact of Islam in the region, there is a tendency 

to view Islam in bipolar terms, the upshot of which is to lump organizations founded on 

Islamic precepts as being radical with a tendency of associating with terrorist bodies. 

This orientation prevents one from discerning between mainstream political Islam and 

its more extremist peripheries. It is therefore refreshing that Dr. Gross does not fall 

prey to this stereotyping and remains strictly objective in his assessment. 

For my part, however, perhaps from having been actively involved in the political 

process pertaining to security matters in Southeast Asia, it would be disingenuous 

to profess non-partisanship in my overall assessment of the situation. I dare say 

that many in the region still view the U.S. policy on terror as being marked by that 

Wilsonian machismo that has led it to miss the woods for the trees. This is not to 

suggest that the terrorism-related discourse is an exercise in futility or that it should be 
vi

abandoned altogether. While it is true that terrorism from afar has stoked the domestic 

radical fi re and led to acts of violence, governments in the region have hijacked the 

war on terror for their own political ends. On the pretext of fi ghting terrorism, many 

regional leaders have blatantly consolidated their political powers, further entrenching 

the insidious forms of soft-authoritarianism that they have consistently opposed and 

sought to reform. 

Just as sound policies for engaging Muslims cannot be formulated without a thorough 

understanding of history, this understanding will not come about from clichéd notions 

of Islam. Dr. Gross’ book, therefore, is not merely an academic exercise but is highly 

instructive in helping to devise an approach for those who have an interest in seeing 

long-term stability in the region. 

 As I have come to know Dr. Gross over the past several months, I have found him 

a scholar with a deep knowledge of Islam. With this book he has made a formidable 

contribution to the fi eld, and I have no hesitation in recommending this work to those 

interested in learning about the role of Islam in the politics of Southeast Asia.

 Anwar Ibrahim

 Washington, DC

Anwar Ibrahim is former Finance Minister and Deputy Prime Minister of Malaysia. 

During academic year 2005-2006, he was Distinguished Visiting Professor at the 

Prince Alwaleed Bin Talal Center for Muslim-Christian Understanding at Georgetown 

University.
vii

A Commentary on

A MUSLIM ARCHIPELAGO: ISLAM AND POLITICS

IN SOUTHEAST ASIA

Allen L. Keiswetter

Dr. Max Gross, a trained historian, has written a baseline history of Islam in 

Southeast Asia. Starting with basic questions such as how did Islam come to this region, 

he connects the interaction of local authorities, colonial powers, and governments 

with the challenge Islam has presented to governance for more than a thousand 

years. Especially strong are the introductory and concluding chapters. The former 

provides a short scan of the history of the expansion of Islam into Southeast Asia and 

of the relationship of colonial legacies of the British, Dutch, Portuguese, Spanish, and 

Americans to Islam today in the region. The last chapter traces the development of the 

idea of an Islamic state from the time of Mohammad in Medina to its present-day role 

in the politics of Southeast Asia.

Still, this is a book with a contemporary focus. Dr. Gross’s purpose is to use history 

to explain today’s Islamic insurgencies in Indonesia, Malaysia, Thailand, and the 

Philippines and to offer perspectives for the future. These four countries fall along a 

spectrum. Indonesia, the world’s largest Muslim country, is about 90 percent Muslim, 

and the confl icts which Dr. Gross examines are largely between a secularization of 

Islam, especially Sukarno’s Pancasila mixing Islam and nationalism, and the much 

more traditional Islamic orthopraxy among the Acehnese and others. Malaysia has 

a different context; its population is 53 percent Muslim, and the central question 

concerns accommodation between the majority Muslims and the minority Christians 

and ethnic Chinese. In Thailand and the Philippines, where the Muslims are minorities 

themselves (approximately four and fi ve percent respectively), the question is political 

accommodation in the opposite direction. Underlying most of these confl icts are 

separatist histories based not only on religious differences but also on geographic, 

ethnic, racial, and social disparities. 

This book’s unique contribution is that it brings together in one reference a mass of 

information on the insurgencies in Southeast Asia. The country accounts are detailed 

and thorough as to events, organizations, dates, and participants. The chronological 

context provides Dr. Gross the opportunity to give his insights about historical causality. 

His accounting highlights the interaction of the insurgencies within Southeast Asia and 

their international connections outside the region. Especially good are the detailed 

presentations in the chapters on Indonesia and the Philippines. 

Against this baseline the stage is set for further research and analysis. Two 

things in particular come to mind. The fi rst is the need to answer further analytical 

questions from the information Dr. Gross has presented. How are the histories similar 

and different and why? What strategies have been most successful in dealing with 

the insurgencies? To what extent is the motivation of the insurgents religious and 
viii

to what extent is it based on other factors? The second involves further inquiry in 

line with the book’s subtitle “Islam and Politics in Southeast Asia.” While politics 

is comprehensively covered, of interest would be additional research about the nonpolitical factors regarding the insurgents, such as their similarities and differences in 

Islamic belief and practice, their economic situations, and their prospects and hopes 

for the future. 

Even a brief glance at the new Army Field Manual on counterinsurgency makes 

clear that the questions answered and inspired by this book are not marginal to the 

concerns of intelligence analysts. In its fi nal draft, its chapter on intelligence concludes 

with the following:

What makes intelligence analysis for COIN [counterinsurgency 

operations] so distinct and so challenging is the amount of cultural 

information that must be gathered and understood. However, to truly 

grasp the environment of operations, commanders and their staffs 

must expend at least as much effort understanding the people they are 

supporting as [they do in understanding] the enemy. All this information 

is essential to get at the root causes of the insurgency and to determine 

the best ways to combat it.

Dr. Gross has made an excellent contribution to what is needed, and further analysis 

and research will, one hopes, provide even further insight. 

Allen L. Keiswetter is a faculty member at the National Defense Intelligence 

College, on contract from Pearson Analytical Solutions, and Adjunct Scholar at the 

Middle East Institute. He teaches courses on Islam and on the Middle East.
ix

A Commentary on 

A MUSLIM ARCHIPELAGO: ISLAM AND POLITICS 

IN SOUTHEAST ASIA

Roger E. Biesel

Islam has come to the forefront of the world’s consciousness following al-Qa’ida’s 

attacks on the United States on September 11, 2001, and subsequently those in London, 

Madrid, and Indonesia. In the West, Revolutionary Islamism has become as reviled an 

ideology as revolutionary Communism was prior to 1991. With Islam as such a potent 

force in international relations, it is apropos that this richly documented and insightful 

work by one of Washington’s leading Islamic scholars should arrive now. In his 

discussion of Islam, Dr. Gross’ focus is not on the Arab world, as some might expect, 

but on that area where the largest number of Muslims in the world dwell—Southeast 

Asia. Because Asia continues to advance as the fastest growing region in the world, 

the author’s focus on the Islamic phenomenon there takes on important meaning.

Dr. Gross is well qualifi ed to address this topic. With a career spanning over 40 years 

as a scholar and lecturer on Islam, he presently provides lectures at U.S. government 

offi ces in Washington. Having traveled widely in the Muslim world, he currently 

serves at the Center for Christian-Muslim Understanding with the faculty of his alma 

mater, Georgetown University. Dr. Gross’ previous work at Washington’s American 

University and George Washington University on Islam, international relations of the 

Middle East, and the Arab-Israeli confl ict is widely recognized. He has published 

extensively on these same subjects while also supporting works of other scholars with 

his informed contributions.

This timely, well-written work is delightfully understandable and an easy read 

despite its size and the complexity of the subject matter. Those who may have thought 

of Islam as a totally Middle East and Arab entity will come away with another point 

of view. The author’s “General Considerations” set the scene, clarifying how the 

ethnic Malay character of the region has created a substantially different approach 

to Islam from that of the Arabs. While Islam in the Arab world and South Asia came 

about largely by the sword and military conquest, Southeast Asia’s experience was 

totally different—largely one of gradual, peaceful assimilation through trade and 

intermarriage. Thus, Islam in Southeast Asia was overlaid onto already existing rich 

and colorful sets of beliefs and tribal superstitions that varied widely from region to 

region. A brief historic overview is followed with discussion of Europe’s impact on 

the region and its infl uence in the formation of the two major Islamic countries in the 

region—Malaysia and Indonesia. For those seeking deeper historical treatment, the 

author addresses the four key Islamic populations in the region—Malaysia, Thailand, 

Indonesia, and the Philippines—up to the present time.
x

Islam’s colorfulness and variety make any broad generalities or characterizations 

about it inaccurate. Similar to Christians, Jews, Buddhists, Hindus, or other faiths, 

most followers of Islam are not fanatics, extremists, or revolutionaries. While all 

Muslims share a common religious belief, their behavior varies widely. One unique 

characteristic of Islam is that it is totally centered on God—state and religion melt 

together. Muslims believe that the Koran, Islam’s holy book, and Muslim law alone 

are adequate to govern the relations of man. Only four truisms apply to Islam: that all 

Muslims believe in the same Abrahamic God that Jews and Christians worship; that 

they believe Muhammad was God’s complete and fi nal prophet; that they believe in 

the power of prayer—fi ve times a day is mandatory; and that they believe in the Last 

Judgment. Beyond that, Dar al Islam, the House of Islam, is more diverse than it is 

homogeneous. The diversity of Islam becomes more understandable when considering 

that some 1.2 billion people of every race are Muslim—from China to Senegal, from 

the former Soviet Union to Nigeria, plus some seven million in Europe and several 

million Americans—with only about 20% Arab.

Since its founding some 1,400 years ago, Islam has been a source of confl ict, 

violence, and fanaticism. The bombings and shootings of the new millennium in 

Southeast Asia that have been killing Muslims by the score and the bloody ShiiteSunni standoff in present-day Iraq are but recent examples. Nevertheless, Islam 

also has been a source of generosity, unbelievable beauty, ingenious technological 

innovation, and inspiration to both kings and the disenfranchised alike.

Dr. Gross’ emphasis on Southeast Asia takes on added meaning when considering 

that two of the world’s three largest Muslim populations reside there—196 million in 

Indonesia, 138 million in Pakistan, and 114 million in Bangladesh. This compares 

with the 350-plus million residing in Arab countries of the Middle East and North 

Africa. In addition, non-Arab countries hosting populations exceeding 50% Muslim 

include Afghanistan, Iran, Mali, Malaysia, and Turkey. Also, many Arabs in Egypt, 

Lebanon, Palestine, and Syria are Christian—not Muslim. Similarly, the vast majority 

of Muslims in Southeast Asia are not “Arabic” despite recent efforts by oil-rich Saudis 

to export their more fundamental Islamic beliefs to the region.

In this age of globalization and global interdependence, tolerance of diversity 

becomes increasingly crucial. A calm, law-abiding Muslim population in the West 

and content, secure, non-Muslim religious minorities in the Islamic world can be 

barriers to the belief that every region belongs to just one faith or culture. Although 

the principle of human rights is reason enough for tolerance, religious diversity will 

safeguard all against the “clash of civilizations,” the clash between Islam and the West 

that extremists want. The fi ssure between two great civilizations which occurred 

during the Crusades in the 1100-1500 time frame has outlived any useful meaning and 

should not be replayed.

As we proceed into the 21st century, leveling the playing fi eld between the West 

and the Islamic world and leaving our grandchildren a legacy of understanding and 
xi

tolerance are absolutely essential, even more so in the Muslim world. Muslims have 

come to experience life in the West in terms of being free to interpret their own religion. 

To resist suspicion of being a “fi fth column,” they need to interact more openly with 

other faiths and in a more generous spirit. For one, they need to stop treating nonMuslim minorities residing in Islamic lands as second-class citizens. Following such 

traditional Muslim theocracy in this regard has no place in a modern Islamic state. The 

assertion that Islam is incompatible with democracy and modernity makes Dr. Gross’ 

latest work all the more important. He helps us place global events and our fears into 

a balanced context—something never more important than it is today.

Roger E. Biesel is a Southeast Asia analyst at the Defense Intelligence Agency who 

has in recent years been focused on the role of Islam in the region.

xiii

AUTHOR’S PREFACE

On 10 -11 September 2003, the Center for the Study of Intelligence hosted a 

conference in Charlottesville, Virginia, to discuss the subject “Intelligence for a New 

Era in American Foreign Policy.” One of the recommendations from that conference, 

in the context of “Proposals for Change” within the Intelligence Community, was as 

follows:

The U.S. government was a big actor in creating the broad and 

institutional knowledge base necessary for conducting the Cold War. 

Could we replicate that in some way today? We need to create, among 

other things, an atlas of Islam...a knowledge base. We ought to do it as 

a national project.1

This research study responds to this recommendation, albeit at a somewhat more 

modest level than “a national project.” Additionally, in order to narrow the focus, the 

current study focuses only on the countries of Southeast Asia—Indonesia, Malaysia, 

the Philippines, and Thailand. The current volume is a projected Volume One of a 

multi-volume study. The fi nal result is intended to be a global compendium, attempting 

to assess the role and place of Islam in the contemporary world. As this work ends, the 

author begins research on a second volume tentatively titled “Islam in South Asia.”

For more than 20 years the author taught a course at the National Defense Intelligence 

College on “Islam in the Contemporary World.” Through the years, students in this 

course have conducted research and written papers on the place of Islam in a country 

of choice. Other students chose a particular Islamist group to examine with an eye 

to assessing its particular signifi cance. Altogether, more than 250 papers have been 

amassed.

The current study is inspired by the efforts of all these students, but is signifi cantly 

supplemented by the author’s own research and experience over even more years 

of study and teaching about Islam. In writing their papers, students responded to a 

standard set of fi ve questions:

How did Islam come to the country? Or how did the country come to be 

predominately Islamic?

How central has Islam (as opposed to other political ideologies) been in the 

political history of the country as it has come into modern times?

What is the offi cial policy of the current government of the country toward 

Islam? Why does the government have such a policy? And what are the 

benefi ts and costs to the government for maintaining such a policy?

1 Central Intelligence Agency, Intelligence for a New Area in American Foreign Policy, Center for the 

Study of Intelligence Conference Report, 10-11 September 2003, Charlottesville, Virginia (Washington, 

DC: Center for the Study of Intelligence, January 2004), 20.

1.

2.

3.
xiv

What principal Islamist movements exist within the country (or in exile) that 

are working to change the current political status quo (or maintain it)? If there 

is more than one, why the multiplicity of movements? What animates the 

adherents of these movements, and what is/are their goal(s)?

What is your prognosis concerning the future of contemporary Islamic 

movements in the country of your study?

The current study follows this same thematic approach, although much integration 

across the region being examined (Southeast Asia) was necessary. A copy of these fi ve 

questions sat before the author constantly during the more than one year required to 

complete this study.

The chief concern about Islam for intelligence personnel and national policymakers is not its spiritual or religious dimensions but rather its political aspects. Since 

the 1979 Iranian revolution, and more particularly since the shocking attacks on the 

New York World Trade Center and the Pentagon in Washington, DC, on September 

11, 2001, this political aspect of Islam has assumed a new importance that was not so 

readily apparent in the earlier decades of the 20th century. Islam as a political factor in 

world politics, particularly in the Muslim world itself, during the post-September 11, 

2001, era is the principal focus of this study. Factors other than Islam—nationalism, 

modernization, globalization, secular political ideologies, and the impact of external 

powers—are of course also part of the political milieu of every Muslim country. The 

aim of this study has been to achieve a balanced assessment in which the impact of 

the Islamic political factor is measured as one of several other factors operating in the 

politics of the Muslim world.

Student authors who contributed to my thinking on Southeast Asia include: Paul 

E. Belt, Shawn P. Boudreau, William R. Bray, Jimmy L. Briggs, Robert J. Briggs, Ray 

M. Ceralde, Shannon L. Cornwell, Robert A. Dahlke, Steven E. Daskal, Howard C. 

Davis, Susan L. Davis, Andrew J. Furne, Mary P. Gibson, Cecil D. Giddens, Robert E. 

Hagen, Richard W. Hayden, Victor R. Jolin, Jason A. Kotara, Jennifer Laun, Kevin M. 

Lucey, Bill A. Miller, Elaine M. Parks, Kelly Parks, Steven F. Rue, Houston S. Roby, 

Rachel Schindel-Gombis, Margaret Silberstern, Sherril L. Stramara, and Danny R. 

Thornton. I have reread each of these student papers in the preparation for this study. 

They will see little of their work in the fi nal product, however, as I found it necessary 

to go far beyond their own modest term papers in my research. Nevertheless, each one 

was a source of inspiration, a source of ideas, and a pointer to useful sources.

As one who has spent a career as a specialist in the Middle East, the author is 

conscious of his limitations in writing about Southeast Asia. However, contact with a 

number of such regional specialists, such as Anwar Ibrahim and Eugene Martin, who 

have read and commented on various parts of the study, has been helpful. Friends 

David Dennis and Jennifer Noyon also have read and commented on different parts of 

the text. I thank my wife, Nasrine, for her patience and support. The author assumes 

full responsibility for any limitations of the study, of which he is sure there are many.

4.

5.

xvi

The Malay Archipelago, a region more commonly known as Southeast Asia.

Source: CIA.
1

CHAPTER 1

ISLAM IN SOUTHEAST ASIA: HISTORICAL BACKGROUND

GENERAL CONSIDERATIONS

The Malay peninsula and Indonesian archipelago of southeast Asia, extending from 

southern Thailand in the west and the southwestern portions of the Philippines in the 

east, constitute a highly populated geographic region where Islam is well established. 

The Muslim Hui people of central China (as opposed to the Uygurs of western China) 

and the Cham people of Cambodia and Vietnam may also be thought of as belonging 

to this same regional grouping. 

Table 1

Muslim Population in Southeast Asia

Country

Total 

Population 

(millions)

Percent 

Muslims

Muslim 

Population 

(millions)

Brunei 0.4 67.2 0.3

Cambodia 13.4 > 0.1 0.1

China 1298 1.4 18.2

Indonesia 238.5 88 210

Malaysia 23.5 52.9 12.4

Singapore 4.4 14 0.6

Philippines 86.2 5 4.3

Thailand 64.9 3.8 2.5

Vietnam 82.7 > 0.01 0.1

Source: Central Intelligence Agency, The World Fact Book, 2004. Washington, DC: Central 

Intelligence Agency, 2004. Intelink URL: http://www.cia.gov/references/csfo/cfactbook/index.html. 

Percentages cross-referenced with Richard V. Weekes. The Muslim Peoples: An Ethnographic Survey

(Westport, CT: Greenwood Press, 1984)

The modern state of Indonesia is the largest country in the world in terms of its 

Muslim population, although at least 12 percent of its population is non-Muslim. 

Malaysia, a much less populous state, is politically dominated by its Muslim Malay 

population, despite the fact that Malay Muslims constitute barely a majority in the 

country. In Thailand and the Philippines, the Muslim populations constitute small 

minorities of about four to fi ve percent. Nevertheless, these minorities are large and 

concentrated enough to be politically signifi cant in each country. The Hui people 

of China, who number approximately 9.2 million, are numerically signifi cant but 
2

constitute less than one percent of the vast Chinese population of nearly 1.4 billion. 

The small Sultanate of Brunei, famous for the fabulous wealth its ruler derives from 

rich petroleum deposits found under its soil, constitutes only a tiny fraction of the 

large Muslim community in southeast Asia. The Cham Muslims of Cambodia, who 

numbered approximately 300,000 in the mid-1970s, saw their numbers drop to slightly 

more than 100,000 due to the intense persecution they suffered at the hands of the 

Khmer Rouge between 1975 and 1979.1

Islam and “Malayness”

In general, the term “Muslim” in southeast Asia also means Malay. Although 

Indonesia and the Philippines together constitute a complex island archipelago 

(Indonesia itself consists of 13,667 islands spread over three time zones, although 

only fi ve of these can be considered major population centers), populated by a large 

number of ethnic groups (more than 50 in the case of Indonesia, more than ten in the 

Philippines, and at least ten in Malaysia), the process of Islamization in the region 

has also been perceived as a process of Malayization in that, particularly in the early 

period of Islamization, the Malay language served as the lingua franca of the loose 

confederation of trading sultanates that fi rmly established Islam in the region. This 

process was unintentionally reinforced by the Dutch administration of the Netherlands 

East Indies that promoted the use of Malay throughout the islands.2 Today, Bahasa 

Indonesia, the formally adopted national language of Indonesia, is but a variant of the 

Malay language spoken in Malaysia (Bahasa Malaysia), whose purpose is to knit the 

multiethnic and multilingual, diverse population of Indonesia together. Similarly, both 

the Muslim minorities in Thailand’s fi ve southernmost provinces of Pattani, Songkhla, 

Satun, Yala, and Narathiwat and the Philippine’s two substantially Muslim-populated 

southwestern regions identify themselves as Malays rather than as Thais or Filipinos. 

Even the Cham Muslims of Cambodia and Vietnam carry identities as being of Malay 

origin. Only the thoroughly Sinicized Hui Muslims of central China lack such a Malay 

identity, although no doubt some of their original numbers were of Malay origin. To be 

a Muslim in southeast Asia, therefore, carries an ethnic as well as a religious identity 

and makes adherence to Islam all the more relevant politically.

The Potential of Malay Unity

The contemporary militant Islamist group in the region, Jemaah Islamiyah, has as 

its stated goal the unifi cation of these Muslim Malay people into a single Islamic state, 

1 ZacharyAbuza, Militant Islam in Southeast Asia: Crucible of Terror (Boulder, CO: Lynn Reinner 

Publishers, 2003), 81.

2 Robert Day McAmis, Malay Muslims (Grand Rapids, MI: William B. Eerdmans Publishing Co., 2002), 

47.
3

comprising not only Indonesia and Malaysia, but also the southern Thai and Philippine 

provinces. There is no indication that the Cham of Cambodia and Vietnam are included 

in this ambition, but Cham Muslims from Cambodia are active in the movement. The 

Hui of China are probably excluded from the Islamist vision of Jemaah Islamiyah, 

but their presence could weigh in with regard to Chinese policy toward the Muslim 

peoples of southeast Asia. The Jemaah Islamiyah and its affi liate groups (e.g., Abu 

Sayyaf in the Philippines) stand accused of numerous acts of terrorism in southeast 

Asia and have been linked to bin Ladin’s al-Qa'ida organization. Accordingly, the 

Jemaah Islamiyah has been targeted in the U.S.-sponsored Global War on Terrorism 

(GWOT) and is strongly opposed by the four major state regimes in the region affected 

by the Jemaah Islamiyah ambition. In the face of such fi erce opposition, it seems 

unlikely that the self-defeating terrorist tactics adopted by the Jemaah Islamiyah can 

have any short-term prospect of success.

The Jemaah Islamiyah vision of a unifi ed Muslim Malay Southeast Asia is not all that 

different, however, from that of revolutionary Indonesian leader Sukarno. His original 

stated objective also envisioned a political union of the same scattered territories, albeit 

under a nationalist, rather than a religious/ideological, banner. Although the original 

BPUPKI3 constitutional document did not include the Muslim portions of Thailand 

nor the Philippines, it did include all of what is now contemporary Malaysia as well 

as Portuguese Timor (East Timor), and subsequent interregional politics suggests that 

the Muslim (Malay) areas of the Philippines and Thailand were not wholly outside 

of Sukarno’s scope. His famous Pancasila doctrine, which remains institutionalized 

in Indonesian constitutional practice, was his way of preempting efforts of some to 

make Indonesia an Islamic state governed by Islamic law (Shari’a) and to base it on 

nationalist principles instead. The result has been the ironic situation in which Malaysia 

with a population that is 53 percent Muslim is “offi cially” an Islamic state, whereas the 

much larger Indonesia with a population that is 88 percent Muslim is not.

The vision of a politically unifi ed East Indies, including the Malay peninsula, 

however, may have been less a Japanese-empowered indigenous political movement 

than a legacy of Dutch imperial attitudes which from the beginning sought a monopoly 

on the spice trade in the East Indies and jealously guarded Holland’s dominant position 

in southeast Asia as best it could. The Netherlands did not prove to be the strongest of 

the competing European imperial powers. It never seriously challenged Spanish control 

of the Philippines, never replaced Portuguese control of East Timor, proved unable to 

3 Badan Penyelidik Usaha Persiapan Kemerdekaan Indonesia (BPUPKI) was a committee established 

under the auspices of the Japanese colonial administration in March 1945, shortly before the surrender of 

the Japanese to the United States on August 15, 1945, to draw up a constitution for an independent, post-war 

Indonesia. The committee members included Sukarno, Muhammad Hatta, and other leading members of the 

Indonesian independence movement that successfully resisted the reimposition of Dutch rule after World 

War II. Japan gained a certain degree of Malay support during the war on both the Malay peninsula and the 

Indonesian archipelago by promising independence and a unifi ed Malay state within the envisioned Greater 

East Asia Coprosperity Sphere following victory against the allies. The vision of Raya Indonesia (Greater 

Indonesia) remained part of Sukarno’s policy throughout his period of rule, which ended in 1965. 
4

challenge Thai hegemony over the northern Malay states, and fi nally proved unable 

to resist British inroads in the territories that were to become Malaysia. The result 

has been a divided region with different governance and administrative traditions that 

constitute more the legacy of the imperial past than of indigenous political evolution.

Factors Promoting Disunity

Yet another factor promoting political disunity has been the variety of autonomy or 

even independence movements that have characterized especially modern Indonesian 

political history. The almost continuous rebellion of Aceh in northwestern Sumatra and 

the independence movement of the Molucca Islands (Republik Maluku Selatan) in the 

mid-1950s are two of the most obvious examples of this tendency. The Darul Islam

movement of the early 1950s in which an effort to establish an independent Islamic 

state governed by the Shari’a in western Java was yet another example of a different 

type. Comprised of thousands of islands, the Indonesian archipelago exhibits powerful 

centripetal political tendencies. When the European powers began arriving in the region 

in the 16th century, what they found was a large number of states — some Islamic 

sultanates, others Hindu/Buddhist rajas. As European power began to wane in the early 

20th century, and especially after World War II, it was perhaps natural that regions of 

the East Indies that had once been states sought to revive their identity as independent 

states. In departing, the Dutch took note of this tendency and sought to empower it. 

Whereas Dutch administrators in the late 19th and early 20th centuries busied themselves 

with consolidating their rule, eliminating legacies of the old independent states that had 

characterized the East Indies and building the infrastructure of a modern, consolidated 

unitary state, as it became clear after World War II that the Dutch could no longer 

maintain their position in the region, they began restoring and recognizing a series of 15 

states (e.g., East Indonesia, West Kalimantan, East Sumatra, Negara Madura, Daerah 

Banjar in Kalimantan (Borneo), Pasundan (west Java), and others). This was in advance 

of signing a treaty with the new revolutionary government of Indonesia that the Dutch 

would do only if the new state was organized as a federal system that continued to 

recognize the Dutch Crown, remained tied to Holland economically, and whose states 

could deal with the Dutch independently.

The ink was barely dry on the December 27, 1949, treaty that transferred sovereignty 

from the Netherlands to the new United States of Indonesia (Republik Indonesia 

Serikat) than the new states the Dutch had created began to dissolve themselves, either 

voluntarily or in response to threats by the revolutionary army of Indonesia. On August 

17, 1950, the federal system, which the Dutch had demanded, was formally abolished 

and a new constitution, closely modeled on the original constitution of 1945 defi ning 

the Republic of Indonesia as a unitary state with a strong central government based in 

Jakarta, was proclaimed. The original consolidating tendency of the Dutch colonial 

authority was restored with subsequent pain and hardship to many citizens of the new 

country who opposed this tendency.

The struggle between the forces of centralization and those of decentralization has 

been a characteristic feature of the history of southeast Asia. Over time, the forces of 
5

centralization have generally prevailed. Whether such a tendency will always be the 

case cannot be known with any certainty. Islam is a factor that works both ways. As the 

history of southeast Asia demonstrates, Muslims desirous of residing in a state where

Shari’a prevails can be satisfi ed with a small state, but they also can labor on behalf of a 

large, strong, centralized state. What tendency Muslims are likely to favor in southeast 

Asia is an important theme of this work.

HISTORICAL OVERVIEW

Role of Trade

Most sources trace the introduction of Islam into southeast Asia back no further 

than the 10th or 11th centuries, but a case can be made that the Arab, Persian, and 

later Indian traders that were the primary propagators of the faith into the region were 

active as early as the 7th century and certainly by the 9th century, when T’ang Chinese 

fashions were all the rage in Abbasid Baghdad.4 Gradually these merchants settled 

in regions where they established their businesses, married within the indigenous 

population, and raised families according to Islamic law. The new faith spread slowly 

among the established Hindu and Buddhist populations of the region, gradually leading 

to the conversion of some local rulers and the establishment of a number of Muslim 

kingdoms (sultanates) throughout the region during the 14th and 15th centuries. The 

fi rst major state of this type to be established was the Sultanate of Malacca in the mid15th century,5 although several other ruling families had converted earlier. With the 

establishment of a strong Muslim state in Malacca as a linchpin for trade throughout 

the archipelago, Islam gradually permeated the ports and capital cities of various other 

kingdoms in the Malay peninsula and eastern archipelago long before effectively 

penetrating the agricultural populations of the interior or the more easterly islands.

Prior to Malacca on the Malay peninsula, a sultanate had been established at Aceh 

on the northwest coast of Sumatra as early as 1250, but following Malacca more 

coastal Islamic states quickly came into being in the late 15th and early 16th centuries: 

Patani in what is now southern Thailand; Johore and Perak on the Malay peninsula; 

Bantam, Mataram, and Demak on Java; Brunei in Borneo; and Makassar in Sulawesi. 

In the 17th century too, inland Muslim sultanates, such as that of Minangkabau in 

4 Marshall G.S. Hodgson, The Venture of Islam, Volume 1 (Chicago, IL: University of Chicago Press, 

1974), 233.

5 B.R. Pearn., An Introduction to the History of South-East Asia (Berhad, Malaysia: Longman Malaysia 

SDN, 1970), 26 – 34. The strategically located Malacca was a center for Arab, Persian, Indian and Chinese 

traders moving their goods between various trade centers. Due to the prevailing winds, Malacca hosted ships 

and their crews for weeks at a time while they waited for winds to shift. Beginning about 1402 Paramesawar, 

a new Hindu Prince of Malacca, began asserting his strength against regional enemies, leading him to 

assert his status as an independent ruler and ultimately declaring himself a Muslim prior to his death in 

1424, taking the name Megat Iskander Shah. That the conversion was contested was evidenced by the 

power struggle between his two sons following his death. The issue was not settled until 1446 when Kasim 

prevailed for Islam and took the name Muzaffar Shah and the title of Sultan. 
6

Central Sumatra, began to be established.6 The movement included what is now the 

Philippines, where Islam was well established on Sulu and Basilan islands and on 

Mindanao in the south and was spreading into the north at the time of the arrival of 

the Spaniards in the 16th century.7 A Muslim sultan by the name of Suleiman had 

just established himself in Manila at the time of the arrival of the Spanish fl eet in 

1571,8 and it is likely the whole Philippine archipelago would have been more strongly 

infl uenced by Islam had the Spanish intervention not occurred.9

Yet another direction of this movement was mainland China, where Arab and 

Persian merchants and mariners also gradually settled in various coastal port cities, 

especially Canton, bringing their religion with them. Marrying local Han Chinese 

women, but raising families within the Islamic tradition, these merchant/traders lived 

in specially designated “barbarian settlements” which may have corresponded to the 

various sultanates being established elsewhere in Southeast Asia. Their numbers only 

increased as families grew and as more foreign Muslims continued to settle in China 

until the 14th century. The establishment of the Ming Dynasty, which overthrew the 

former Mongol dynasty in 1368, led to a period of severe backlash against foreign 

presence in China, in which Muslim immigrants were forced either to depart or 

assimilate (abandon foreign languages). Barbara Pillsbury notes, “It was during this 

period (the Ming Dynasty, 1368 – 1644) that the Muslims in China became Sinicized, 

acculturating to Han Chinese ways through the adoption of Han surnames, clothing 

and food habits and through speaking Chinese as their everyday language.”10 They 

did not abandon their religion, however, but continued to increase in numbers, even 

as they became “increasingly similar, physically as well as culturally, to the Han.”11

Gradually, the Muslims ceased to be thought of as foreigners, but a unique Chinese 

people, the huihui, or Hui, as opposed to the vast Han majority in China.

The partial Islamization of the Champa kingdom in central Vietnam followed 

this same pattern. Originally established as a Hindu kingdom by Malay immigrants 

originating in today’s Indonesia, probably from Aceh, the Champa kingdom, whose 

capital was at Indrapura (Tra Kiêu) near modern Da Nang, fl ourished from the 5th 

6 Anthony H. Johns, “Indonesia: Islam and Cultural Pluralism,” in Islam in Asia: Religion, Politics and 

Society, ed. by John L. Esposito (New York: Oxford University Press, 1987), 205.

7 Lela Garner Noble, “The Philippines: Autonomy for the Muslims,” in Islam in Asia: Religion, Politics 

and Society, ed. by John L. Esposito (New York: Oxford University Press, 1987), 97.

8 Charles Kimball, “The Long Road from Mecca to Manila,” in History of Thailand and Southeast Asia. 

URL: http://www.guidetothailand.com/thailand-history/mecca_manila.htm. The name Manila is allegedly 

derived from the Arabic term Ma’man Allah (safe/secure place of Allah). Ismail al-Farouki. “Islamic 

Renaissance in Contemporary Society,” in Muhammad Mumtaz Ali, ed., Modern Islamic Movements: 

Models, Problems and Prospects (Kuala Lumpur: A.S. Noordeen, 2000), 5.

9 Ira M. Lapidus, A History of Islamic Societies (Cambridge, UK: Cambridge University Press, 1988), 

469 – 470, provides an excellent account of the Islamization process in Southeast Asia.

10 Barbara Pillsbury, “Hui” in The Muslim Peoples: An Ethnographic Survey, ed. by Richard V. Weekes 

(Westport, CT: Greenwood Press, 1984), 333.

11 Pillsbury, “Hui,” 333.
7

century C.E. until 1471, when it was destroyed by the Vietnamese in the course of 

that kingdom’s southward expansion. At that time most of the Cham who had become 

Muslim fl ed to Angkor (modern Cambodia), where they were given refuge by the Khmer 

king. There they continue to live today in scattered, isolated Muslim settlements in the 

larger Buddhist, Khmer culture. Before the fall of the Champa kingdom, its prosperity 

had rested in involvement in the east -west trade between China and India, plus a 

kinship and perhaps religious alliance with the Malays of Malacca and the Indonesian 

archipelago to which they were closely linked both politically and economically.12

A small number of Muslim Cham continues to reside in central and southern coastal 

Vietnam.

Role of Islamic Schools/Missionary Activity

A primary means by which Islam spread throughout southeast Asia was the pondok

(pesantren in Indonesia), a Malay term for an Islamic religious school corresponding 

to the madrasa in the central Islamic lands. Hajj Ahmad Kamar suggests that “people 

were attracted by provisions in the Qur’an and the Hadith that mankind should be 

ranked on a basis of interpersonal equality,”13 that is, by the egalitarian ethos of the 

faith as opposed to the rigid caste structure associated with Hinduism. Islam was spread 

by ‘ulama who opened such religious training centers, where they trained students in 

Islamic doctrine. The students then returned to their district villages and communities, 

where they in turn spread the word of the Qur’an. The connection of Islam with the 

seagoing international trade of the era was also clearly relevant.14

Role of Sufi sm

Most sources agree that the Islam the native Malay population of this region found 

agreeable and attractive was also closely associated with Sufi (Islamic mysticism) 

teachings or, perhaps more apt, with that understanding of Islam that enables the believer 

to maintain diverse approaches to the experience of religious truth while affi rming 

the oneness of God and the truth of the Islamic message. The association of Islam 

and mysticism enabled converts to maintain elements of traditional Hindu-Buddhistanimist practice and also accept the basic values and tenets of Islam as well. The result 

has been an Islam that has been historically syncretic and characterized by tolerance 

of diverse points of views, combined with legacies of pre-Islamic practice. The noted 

British anthropologist Clifford Geertz provided an example of this syncretism from a 

fi eld visit he made to Java in 1960. A typical prayer offered by a Javanese villager to 

12 Ronald Provencher, “Cham” in Richard V. Weekes, ed., Muslim Peoples: A World Ethnographic 

Survey, 2d ed. (Westport, CT: Greenwood Press, 1984), 199.

13 Hj. Ahmad Kamar, “Islam in Peninsular Malaysia,” in Muslims in China and South-East Asia. URL: 

http://www.erols.com/zenithco/index.html. Accessed 10 April 1998.

14 For an excellent discussion of the Islamization process in Southeast Asia, see Lapidus, History of 

Islamic Societies, 469.
8

begin a feast included invocations to the guardian spirits of the village, the household 

angel of the kitchen, the ancestors of all the guests, and the spirits of the fi elds, waters, 

and a nearby volcano. But the prayer ended dramatically with the phrase, “There is no 

god but Allah and Muhammad is the Prophet of Allah.”15

ENTER THE EUROPEANS

It is diffi cult to estimate the spread of Islam in Southeast Asia by the time of the 

arrival of the West European powers in the region in the 16th century. What fi rst the 

Portuguese, then later the Spanish, the Dutch, and the English merchantmen who 

explored these lands, found was a series of mainly coastal Muslim sultanates which 

dominated the east -west sea trade routes that linked China with India and the Middle 

East beyond, but remained in competition with other Hindu and Buddhist kingdoms 

that still existed in the region. What is clear, however, is that entry of the Western 

powers into southeast Asia helped to spur the advance of Islam over the next few 

centuries, even as the Europeans consolidated political and economic control over 

the region. As the Europeans made use of missionaries to attempt to win the hearts 

and minds of natives to support European colonial rule, so also Islamic missionary 

activity proved even more successful in promoting a unifying mechanism for resisting 

the permanence of European rule. As a result, although the Europeans succeeded until 

the 20th century in dominating southeast Asia politically, militarily, and economically, 

they proved unable to dominate the region culturally.

On the other hand, the modern states of southeast Asia owe their existence more to 

the interaction of West European powers in the region during the 16th to 20th centuries 

than to indigenous political evolution. The Philippines as a state are that collection of 

East Indian islands over which Spain was able to establish authority beginning in the 

16th century. Indonesia is a product of Dutch control, whereas Malaysia (including 

its provinces of Sabah and Sarawak on the Indonesian island of Borneo) is a legacy 

of British colonial rule. Thailand (Kingdom of Siam) remained relatively free from 

European imperial outreach and indeed was often a very strong kingdom capable 

of exerting imperial ambitions of its own over parts of the Malay peninsula. As a 

result, when each of these states emerged from European colonial control as modern, 

independent nation states in the mid-20th century, the multi-tribal and multiethnic, 

yet nearly overwhelmingly Malay and Muslim, population of the region was almost 

irrevocably divided by modern boundaries and different governing and administrative 

traditions.

Portugal

The fi rst European colonizers on the scene were the Portuguese. Their success 

at capturing Malacca in 1511 had the effect of disrupting the unity of the Muslim15 Clifford Geertz, The Religion of Java (Chicago: University of Chicago Press, 1960), 40 – 41.
9

dominated network of trading states centered upon this strategic city that had come 

into being during the 15th century. Nevertheless, the Portuguese were unable to assert 

control or even ascendancy over the whole region. Instead, they pursued a policy of 

shifting alliances with native Muslim and Hindu rulers to shore up and maintain their 

position against others who sought to dislodge them, especially the Sultanate of Aceh, 

which remained a constant threat to Portuguese control of Malacca during the period 

of Portuguese rule.16

Spain

Another key competitor to Portugal at this time was Spain, whose fl eet, sent from 

Mexico in 1565, began to take control of the Philippines (named after King Philip II 

of Spain). It eventually displaced in 1571 the Sultan of Manila, whose former seat 

of authority was made the seat of Spanish rule in the colony. Unlike the Portuguese, 

who used missionaries relatively unsuccessfully in an effort to convert native Malays 

and draw them into loyalty to Portuguese rule, the Spanish used the Church as 

a mechanism of administration in the Philippines. Although economic and trading 

interests were of concern, ultimate conversion of Filipinos to Christianity was a major 

goal of Spanish policy. Overall, Spain’s occupation of most of the Philippine Islands 

occurred with very little bloodshed, because the native inhabitants offered little armed 

resistance. Two areas that did offer resistance, however, were the Igorot, the highland 

tribal peoples on the main northern island of Luzon, and the Muslim inhabitants of the 

southern areas of Mindanao, Basilan, and the Sulu archipelago. Both of these peoples 

remained detached and alienated from Spanish rule in the Philippines until its end in 

1898, with the Moors, or Moros, as the Spanish labeled them, preferring independence 

from Spanish rule and providing unceasing resistance to Spanish control.

Spain also moved in quickly on various Portuguese interests, taking over the island 

of Ternate in the eastern Spice Islands in 1574 following a popular revolt against the 

Portuguese governor and in 1578 successfully placing its own candidate of choice as 

the new Sultan of Brunei on the north coast of Borneo. The sudden death in 1578 of 

the King of Portugal in Morocco led King Philip II of Spain to assert a personal claim 

to the throne of Portugal, which he succeeded in having recognized in 1580. Under 

Philip, Portuguese colonial interests in Southeast Asia were not vigorously pursued, 

but rather than slowly falling before Spanish ambitions it was now the Netherlands 

and England, both enemies of Spain in this era, that quickly moved in on Portugal’s 

interests in the region.

16 On the Portuguese effort in Southeast Asia, see Lapidus, History of Islamic Societies, 470 – 471, and 

Malaysia: A Country Study, 17 – 20. 
10

Holland

Following the Dutch declaration of independence from the Spanish empire in 1581 

and the English defeat of the Spanish Armada in 1588, both Holland and England 

emerged as signifi cant maritime powers, building faster and better ships than the 

Spanish or Portuguese. In Southeast Asia the Dutch in particular moved quickly to 

seize Portuguese possessions. The Dutch United East India Company, established 

in 1602 and chartered by the Dutch parliament, was the agency for advancing these 

interests. In 1619, the Company, which had forged alliances with the Sultans of Johore 

(Malaysia) and Aceh (Sumatra) against the Portuguese, established a permanent base 

at Batavia (modern Jakarta) on the north coast of Java, from which they sought to 

control the sea lanes through the archipelago. In January 1641, in coordination with 

the Sultan of Johore, the Dutch fi nally were able to overcome the Portuguese fortress 

at Malacca. Henceforth, the Dutch were the preeminent European power controlling 

trade in Southeast Asia and dominating local rulers until the coming of the English in 

the latter decades of the 18th century.17

England

Concentrating its attentions on the Indian subcontinent, the English East India 

Company was content not to compete seriously with the Dutch in southeast Asia until 

increased trade between southern China and English India in the mid-18th century led 

the Company in 1773 – 75 to seek basing facilities on the northern coast of Borneo, 

where the Dutch had shown little interest, and on the Sulu archipelago whose sultan, 

though technically a subject of the Spanish governor in Manila, remained eager to 

assert his independence. A decade later, in 1785, the Company moved to establish 

a permanent naval base in the eastern Indian Ocean, negotiating a treaty with the 

Sultan of Kedah on the northern Malay Peninsula in which it was granted the Island of 

Penang. In this case the Sultan of Kedah was seeking an alliance that would strengthen 

his hand against the king of Siam (Thailand), to whom he was tributary. The 1795 

occupation of Holland by the forces of revolutionary France strengthened the English 

hand further, when the Dutch government in exile in London agreed to permit English 

offi cials to take over all Dutch territories overseas temporarily in order to deny them 

to the French.

A key fi gure at this time was Thomas Stamford Raffl es, an English East India 

Company offi cial, stationed at Penang, who became lieutenant governor of Java 

during the period of temporary English rule over the Dutch East Indies. Unhappy 

with his government’s decision to return the East Indies to Holland after the demise 

of Napoleon, he played a shrewd political game with the Sultan of Johore (Malaysia) 

who, in 1819, leased to the English East India Company the right to establish a 

settlement on the swampy and largely uninhabited island of Singapore. In a very short 

17 On Dutch operations in Southeast Asia, see Lapidus, History of Islamic Societies, 471– 473.
11

time, this settlement fl ourished, in part because of its highly strategic location on the 

Strait of Malacca, but also due to Raffl es’ own excellent administrative abilities, and 

became the dominant trading entrepôt of the region. Unable to resist these English 

inroads into its previously unchallenged domain, Holland agreed in 1824 to an AngloDutch treaty which defi ned the Malay peninsula and Singapore as being in the English 

sphere of infl uence, and England accepted the remainder of the Dutch East Indies 

that eventually became Indonesia as being solely a sphere of Dutch infl uence. On this 

basis, the groundwork was laid for the eventual establishment of the two major Malay 

states: Malaysia and Indonesia.

THE FORMATION OF MALAYSIA

Consolidation of English Authority

In 1826, following the treaty with Holland, the English joined their fi ve coastal 

holdings on the peninsula (Penang, Wellesley [Perei], Dindings, Malacca, and 

Singapore) into a single administrative unit called the “Straits Settlements.” At fi rst 

headquartered in Penang, the administrative center was soon moved to Singapore in 

1832. A subordinate unit of the English East India Company headquartered in Calcutta 

until 1857, the Straits Settlements was then taken over by the British Indian government 

until being made a Crown Colony under the Colonial Offi ce in 1867.

The remainder of the peninsula consisted of the ten sultanates (including Patani, 

today a part of Thailand) into which it had been divided for years. From the perspective 

of the King of Siam (Thailand), however, these Islamic states had been established in 

traditional Thai lands, and with the retreat of Dutch power in the peninsula the Siamese 

king sought to assert Thai primacy over as many of them as possible. The Malay 

sultans responded by seeking English support for their independent status. Fearful 

of offending the King of Siam whose alliance the English wished to maintain against 

Burma, or later against the French in Indochina, yet not wishing to create hostile 

neighboring Islamic states, the various governors of the Straits Settlements walked a 

tightrope of diplomacy throughout the 19th century with regard to the Malay states. 

The long-term result was deeper and deeper involvement in the affairs of the Malay 

sultans until 1874, when the English governor at Singapore succeeded in beginning 

the process of establishing, in exchange for English support, English residents whose 

counsel “must be asked and acted upon on all questions other than those touching 

Malay custom and religion.”18 The fi rst residents were established with the west 

coast Sultans of Perak, Negeri Sembilan, and Selangor. Later, in 1888, the Sultan of 

Pahang, a large east coast state, also requested and received a resident. The remaining 

six Malay sultanate — Kedah, Terengganu, Kelantan, Perlis, and Patani — all in the 

north and paying tribute to the King of Siam, as well as Johore in the south, next to 

Singapore, held aloof and refused to accept an English resident. The northern states 

were the poorest and least developed on the peninsula and have remained so until 

18 Malaysia: A Country Study, 30.
12

today, whereas Johore was and remains relatively prosperous. The sultans of each, 

however, resisted compromising their independence to the English, even after 1909, 

when King Chulalongkorn of Siam ceded to England suzerainty over all the northern 

sultanates except Patani.

Mechanisms of English Supervision

The resident system did have the impact of reducing the independence of the sultans 

that accepted them. The English residents “scrupulously maintained the etiquette and 

ceremony of Malay courts and gave government employment” to the relatives of the 

sultans and their retainers.19 Meanwhile, payment of subsidies to make up for lost 

revenues that accrued from such English-desired reforms as the abolition of slavery 

or the suppression of piracy had the long-term impact of transforming the sultans and 

their governments into appendages of the English administration.

The grouping of four so-called “protected” sultanates into a State Council headed 

by the governor of the Straits Settlements, but from which the fi ve “unprotected” 

sultanates held aloof, formed the basis of the future government of Malaysia. Through 

the State Council the British residents were gradually able to introduce modern 

Western concepts of governance and administration. Finally, in 1896 the British 

administration was able to persuade the sultans under their protection to sign a formal 

Treaty of Federation, which established a federal, but nevertheless unitary, central 

government headed by a so-called Resident General, a single British offi cial in charge 

of the residents of each of the Federated Sultanates and appointed by the Governor of 

the Straits Settlements. In this manner a British-controlled central government was 

brought into being, but the appearances of traditional Muslim governance were also 

maintained. In 1909, Kuala Lumpur was selected as a seat of government for a new 

Federal Council, headed by the Resident General, who was entrusted with modern 

governance responsibilities for what was now called the Federation of Malay States.

Economic Transformation

This political transformation was closely associated with economic developments 

that were taking place during this same period. The rapid expansion of the tin mining 

industry after 1848, then of rubber plantations beginning in the early 20th century, and 

fi nally of iron mining and palm oil plantations, radically transformed the traditional 

pastoral Malay economy centered around small village life. The wealth generated by 

this economic development eased the political change that gradually transformed the 

sultans under British protection into something more like government functionaries 

than independent rulers.

19 Malaysia: A Country Study, 30.
13

At the same time, economic change had far less social impact on the rural Malay 

way of life than might have been expected. Because Malays were generally perceived 

not to be suffi ciently adaptable to work in the new industrial sectors of the Malay 

economy, the British, other Western, Chinese, and Japanese investors who provided 

capital to fund these new economic ventures relied heavily on the import of Chinese 

labor, which greatly augmented the small, already established Chinese community that 

lived in many coastal towns of the Malay peninsula, especially the Straits Settlements. 

The British also relied heavily on immigrants from India and Sri Lanka who served 

in the British police and armed forces of the Malay Federation. Indian immigrants 

also played many private sector roles as well, such as truck, bus, and taxi drivers, 

night watchmen and rubber plantation workers. This immigration was so substantial 

that by the 1930s the demographic portrait of the Malay peninsula had changed 

radically. Whereas the population at the beginning of the 19th century had been 

almost wholly Malay, by the mid-20th century Malays constituted only about 50 

percent in their own country, Chinese about 35 percent, and Indians (both Hindu 

and Muslim) 10 percent. This major demographic change would also have serious 

political ramifi cations in the future.

The economic and demographic changes noted above were confi ned almost entirely 

to the west coast of the Malay peninsula, within the area defi ned as the Federation of 

Malay States. The unfederated Malay states along the east coast were far less affected, 

the population consisting almost entirely of Malay rural villagers living in settlements 

of less than 1,000 people. The same condition was generally true of the two territories 

on North Borneo — S abah and Sarawak — that were also to become part of modern 

Malaysia. These were originally parts of the Sultanate of Brunei whose ruler, in 1841, 

in return for services rendered in helping suppress a local revolt against him, awarded 

the western territory — today called Sarawak — to James Brooke, a former British 

East India Company offi cer and man of independent wealth, in return for an annual 

subsidy. This concession remained in the hands of the Brooke family until 1946, when 

Britain transformed Sarawak into a Crown Colony. 

The territory to the northeast of Brunei (later to be called Sabah) the sultan leased 

in 1865 to a United States venture, the American Trading Company of Borneo. This 

company failed, however, and sold its lease to a Hong Kong-based British fi rm that 

eventually took the name British North Borneo Company. The European investors 

soon found themselves in a dispute with the Sultan of Sulu (Philippines), who also 

laid claim to the leased territory that he argued the Sultan of Brunei had no right to 

lease. The situation was complicated by the determination of the Spanish rulers of 

the Philippines to force the submission of the Muslim Sultan of Sulu once and for all 

and to annex all territories claimed by him, including the land controlled by the North 

Borneo Company. To protect this British interest, the British government granted the 

company a royal charter in 1881. An 1885 treaty among Britain, Spain, and Germany 

fi nally settled the dispute by recognizing Spanish control of Sulu in exchange for 

Spain’s dropping any claims to territory in Borneo. The British then moved quickly 

to establish, in 1888, a protectorate arrangement, similar to that already in effect for 

the federated Malay states, with Sarawak, the Sultan of Brunei, and the British North 
14

Borneo Company jurisdiction, and in 1891 an Anglo-Dutch arrangement delineated 

a border agreement between Dutch and British territories on Borneo. The way was 

made, therefore, for these territories (except for Brunei) to become part of modern 

Malaysia in 1963.

Continuing Role of Malay “Custom and Religion”

A feature of British governance in Malaya was careful avoidance of questions 

“touching on Malay custom and religion” that remained in the hands of the traditional 

sultans. An important result of this policy was the strong persistence of traditional 

society and Malay customs and mores, particularly in the poorer but more independent 

states of the “unfederated sultans” (Perlis, Kedah, Terengganu, and Kelantan in the 

north, and Johore in the south). In contrast, the peoples of the Federation of Malay 

States as well as the Straits Settlements were undergoing rapid social and economic 

change associated with the development of big businesses, improved transportation 

networks, electrifi cation, better public health facilities, and greater educational 

opportunities. The primary agents as well as the chief benefi ciaries of these changes, 

however, were the growing European, Chinese, and Indian immigrant communities, 

far more than the Malays themselves. Increasingly, the lands of the Malay peninsula 

were becoming a complex, pluralistic, and bifurcated society over which the Malay 

sultans, in cooperation with the British, continued to be dominant politically, but in 

which the immigrant communities were dominant economically and commercially.

Growth of Diversity in English Malaya

Not surprisingly, as the Malay peninsula moved closer to political independence 

during the 1940s and 1950s, this imbalance became a prominent issue. Emerging 

political parties tended to be ethnically based, with Chinese and Indian parties 

generally seeking greater political infl uence and Malay parties seeking an 

improved economic status for the indigenous Malay population, but not at the cost 

of reduced Malay political status. The Japanese occupation during World War II 

(1942 – 1945) greatly aggravated ethnic relations, particularly between the Malays 

and the Chinese. Closely allied with the British and mainland Chinese, the Chinese 

community bitterly opposed the Japanese occupation, and resistance groups against 

it were predominately Chinese in composition and leadership. To curry local support, 

the Japanese demonstrated strong favoritism toward Malays and sought to empower 

a growing Malay nationalist movement that went so far as to envision an eventual 

political union with the Indonesian archipelago. The animosities raised during the war 

did not end with the defeat of the Japanese in 1945, but continued to animate Malayan 

politics for a number of years to come. 
15

World War II

The relative ease by which the Japanese overran the British in the Malay peninsula 

and the Dutch in the East Indies in 1942 gravely weakened the prestige of both colonial 

powers in the eyes of the local populations. The weak post-war fi nancial positions 

of both European powers, as well as the war weariness of their citizens, moreover, 

made it diffi cult to restore their former authority in both areas. Yet both tried. As the 

British returned to the Malay peninsula, the government was determined to weaken 

the status of the Malays who were perceived to have collaborated with the Japanese 

during the war. In April 1946 it announced the creation of a new entity called the 

Malayan Union that united the former federated and unfederated states — along with 

Penang and Malacca of the former Straits Settlements — into a single Crown Colony 

under a British governor, and in which the former quasi-independent sultanates were 

totally suppressed. Singapore was withheld from the Union as a separate British 

Crown colony. The Union arrangement, moreover, defi ned all inhabitants of the new 

political entity as equal citizens, regardless of ethnicity, and English along with Malay 

was adopted as offi cial languages of the country.

Assertion of Malay Hegemony

This step by the British authorities provoked a powerful and unifi ed reaction among 

Malays, who feared that such a system would entrench ethnic Chinese domination of 

the economy and lead to Chinese political domination. In March 1946, even before 

the proclamation of the Malayan Union, a general meeting of Malay organizations 

was convened in Kuala Lumpur for the purpose of opposing the Union. The chief 

result of the meeting was the establishment of the United Malay National Organization 

(UMNO), a political party that succeeded in combating the Malayan Union, led the 

country into independence, and continues to be Malaysia’s leading political party 

through today.

The formation of the UMNO was challenged by a counter-organization of non-Malay 

fi gures and secular political parties called the All-Malayan Council of Joint Action 

(AMCJA), which supported the Malayan Union, at least in principle. The association 

of the Malay Communist Party (CPM) with the Chinese-dominated organization, the 

insistence by the AMCJA that Singapore with its large Chinese majority be included 

in the Malayan Union, as well as the unifi ed forcefulness of the Malay-dominated 

UMNO soon led the British to reverse their policy. In February 1948, the colonial 

authority announced the formation, in place of the Malayan Union, of a Federation of 

Malaya. In this new formula, the nine Malay sultans retained their former status and 

powers, especially with regard to Malay customs (adat) and religion. Joined with them 

were two new states, Penang and Malacca, formerly part of the Straits Settlements, 

which would have elected governors rather than hereditary sultans. Singapore with its 

1.5 million Chinese inhabitants remained apart from the federation as a British Crown 

Colony, which ensured a Malay majority in the new Malay state.
16

The “Emergency”

The change in British policy emboldened the opponents of this policy, especially 

the Malaysian Communist Party and other left-wing groups, which so recently 

had been engaged in insurgent operations against the Japanese, to resort to “armed 

struggle” in an effort to overturn the established — as they viewed it — Anglo/Malaydominated society and replace it with a more egalitarian political order as envisioned 

in the Malayan Union. “Terrorist” operations against remote rubber plantations and 

mines, culminating in the assassination of the British High Commissioner in October 

1951, began almost immediately after implementation of the federation plan, leading 

the British in June 1948 to proclaim a state of emergency. The “Emergency,” which 

was declared at an end only in 1960, although it was basically contained by the early 

1950s, had the impact of delaying self-rule for the Federation that Britain had promised 

in 1948, but it did not stop it.

Movement toward Independence

In 1954, negotiations aimed at granting Malayan self-rule resumed, but the issue 

of communal equality remained a principal obstacle. In light of the Emergency and 

the sweep of Chinese Communist-inspired insurgencies in East Asia, the Malays were 

more insistent than ever that non-Malays not be granted full citizenship, and that proMalay economic incentives be institutionalized. The British continued to take the view 

that ethnic Chinese and Indians that had been in Malaya for generations were in fact 

there to stay and should be considered full citizens with equal rights in the country. 

Compromise was fi nally achieved by UMNO leader Tunku Abdul Rahman,20 who 

formed an alliance relationship with counterpart conservative parties — the Malayan 

Chinese Association (MCA) and the Malayan Indian Congress (MIC) — in the other 

major Malayan ethnic communities. Together these parties proved able to dominate 

federal elections, both at the local and national levels, and to reach a compromise 

on ethnic issues that was minimally acceptable to all parties. These principles were 

enshrined in a Constitution drawn up between June and October 1956 and implemented 

on August 15, 1957, when the independence of Malaya was announced.

Independent Malaya

In the Constitution, the issue of citizenship was addressed by defi ning all persons 

born on the peninsula as citizens and requiring naturalization for all others. Malay 

desires were satisfi ed by the formal adoption of Malay (Bahasa Malaysia) as the 

20 Tunku Abdul Rahman, a member of the family of the Sultan of Kedah and a graduate of Cambridge 

University, became leader of UMNO in 1951, succeeding Dato Onn bin Ja’afar who resigned from the party 

after his failure to transform it from an all-Malay organization into a multiethnic party. Malaysia: A Country 

Study, 52.
17

offi cial national language21 and of Islam as the offi cial religion of the state, although the 

freedom of the other religious communities was also guaranteed. The traditional role 

of the sultans was fi nessed by establishing the state as a constitutional monarchy. By 

the terms of the Constitution, the nine sultans chose one of their own as the paramount 

ruler, or king (yang di-pertuan agong), every fi ve years. Although the King and the 

sultans retained their traditional privileges “touching on Malay custom and religion,” 

they were otherwise made subordinate to a prime minister who was to be chosen by 

a popularly elected House of Representatives (Dewan Rakyat). The constitution also 

provided for an appointed Senate (Dewan Negara) with limited powers similar to those 

of the British House of Lords. Besides these provision, the Constitution also retained 

“special privileges for Malays in the civil service, scholarships, business enterprises, 

licenses, and the reservation of some land for their exclusive use.”22

Table 2

Malaysian Kings 

(Yang Di-Pertuan Agong)

Name of Individual Dates as King Hereditary Title

Abdul-Rahman 1957 – 1960 Sultan of Negeri 

Sembilan

Hisamuddin Alam Shah 1 Apr – 1 Sep 1960 Sultan of Senangor

Syed Putra 1960 – 1965 Raja of Perlis

Ismail Nasiruddin 1965 – 1970 Sultan of Terengganu

Abdul Halim 1970 – 1975 Sultan of Kedah

Yahya Petra 1975 – 1979 Sultan of Kelantan

Ahmad Shah al-Mustain 

Billah 1979 – 1984 Sultan of Pehang

Iskandar 1984 – 1989 Sultan of Johore

Aylan Mahibbudin Shah 1989 – 1994 Sultan of Perak

Jaafar 1994 – 1999 Sultan of Negeri 

Sembilan

Salahuddin Abdul-Aziz Shah 1999 – 2001 Sultan of Selangor

Syed Sirajuddin 2001 – Present Raja of Perlis

Source: Table constructed from web pages associated with URL: http://en.wikipedia.org/wiki/Yangdi-Pertuan_Agong. Accessed 1 December 2004.

21 English was also considered a national language for a 10-year period.

22 Malaysia: A Country Study, 53.
18

Singapore remained apart from the now independent Federation of Malaya, but 

it too was granted self-rule as part of the British Commonwealth in 1959. Now 

free to pursue an independent policy, its new Chinese leader, Lee Kwan-Yew, head 

of the island’s left-wing People’s Action Party (PAP), advocated incorporation into 

the Federation upon which resource — poor Singapore was dependent for almost 

everything, including its water, food, and electricity. Fearful that the large Chinese 

population of the island would tip the demographic balance against Malay dominance, 

the Malayan government remained reluctant. A British-sponsored suggestion that the 

inclusion of Crown Colonies Sarawak, Brunei, and North Borneo (Sabah), as well 

as Singapore, into an enlarged Federation, a step that helped to maintain the ethnic 

balance, tended to neutralize Malay opposition. Accordingly, following a lengthy 

political process which included amendments to the Malay Constitution to protect the 

rights of the Iban, Kadazan, and other ethnic minorities in the Borneo territories, and 

a referendum in each of the joining states, the merger was fi nally achieved with the 

formal establishment of the enlarged state of Malaysia on September 16, 1963.

Malaysia

The merger joined the original nine Malay sultanates, each characterized by a 

hereditary ruler, with the three former Straits Settlements — Penang, Malacca, and 

Singapore — and two states in North Borneo-Sarawak and Sabah-each of which was 

headed by an elected governor. Only the Sultanate of Brunei chose not to join the 

Federation. Increasingly wealthy from the revenues generated by the substantial 

oil reserves in his small territory, the sultan preferred not to be one of ten equal 

hereditary members of the Federation nor to share his oil wealth at the decision of 

the federal government. The adherence of Singapore to the Federation also proved 

to be short-lived. Despite efforts of its governor, Lee Kwan-Yew, to demonstrate 

the “Malay” character of the Chinese presence in Singapore and Malaysia, his real 

agenda was to achieve ethnic equality of all the Malaysian peoples, an attitude many 

Malays perceived as threatening to the special privileges they held in the Malaysian 

Constitution. Accordingly, in August 1965, just two years after the merger of Singapore 

into Malaysia, the two decided on divorce by mutual consent, and the island resumed 

its status as an independent, sovereign state.

Opposition to Independent Malaysia

The new Malaysian state did not come into being without signifi cant opposition, 

however. The enthusiasm of the inhabitants of Sarawak and Sabah was far weaker 

than the proponents of the merger had expected, and the Sultan of Brunei succeeded 

holding aloof from it. The incorporation of Singapore proved unworkable as well. Still 

another opponent was the government of the Philippines, which resurrected the claim 

that Sabah was Filipino territory on the grounds that it originally had been part of the 

Sultanate of Sulu. Although Philippine President Diosdado Macapagal (1961 – 1965) 

formally accepted the results of the Sabah referendum that favored joining the North 
19

Borneo territory to Malaysia, the issue remained a bone of contention between Kuala 

Lumpur and Manila for a number of years.

The major opposition to the enlarged Malaysian state was the government of 

Indonesia, then headed by President Sukarno. Strongly imbued with an anti-colonialist 

orientation that perceived the division of the Malay world to be the result of European 

imperialism, Sukarno was a champion of a “greater Indonesia” (Raya Indonesia) 

concept that hoped to unify the entire Malay world, from Patani in southern Thailand 

to Mindanao in the southwest Philippines, into a single Muslim Malay state under his 

own leadership. A revolutionary leader who had displaced the Dutch from Indonesia, 

Sukarno perceived Malaysia to be largely a British creation aimed at frustrating 

Malay union and its expansion into the “Indonesian territories” as an exercise in 

“neocolonialism.” Unable to prevent the expansion of Malaysia by diplomatic means, 

he infi ltrated Indonesian soldiers into Sabah, Sarawak, Singapore, and the Malay 

peninsula, where, within hours of the proclamation of the Federation of Malaysia in 

September 1963, they began to carry out acts of sabotage and terrorism. The aim 

was to spark a popular uprising against the government of Malaysia and in favor of 

union with Indonesia. The effort failed, but left Indonesia and Malaysia in a state of 

confl ict until the overthrow of Sukarno on September 30, 1965. As it gradually became 

clear that the new military government of Indonesia under General Suharto had ended 

Sukarno’s policy and accepted the new political status quo in the region, a treaty of 

peace and mutual recognition that brought a formal end to the hostilities was signed 

on August 11, 1966.

THE FORMATION OF INDONESIA

When after the defeat of Napoleon the Dutch returned to the East Indies in 1816, it 

was the Dutch government that reasserted colonial rule rather than the Dutch United 

East India Company that had been dissolved in 1799, and ownership of all Company 

properties had been assumed by the government of the Netherlands. Whereas the 

Company, operating out of Batavia (Jakarta), rather like one of the many other states 

on Java and the other islands of the archipelago, had working relations — sometimes 

friendly, sometimes hostile — with the sultans and rajas of these states and mainly 

sought to obtain profi ts as well as a dominant position politically and militarily, the 

new governor-general of all Dutch possessions in the East Indies came as a ruler with 

a bureaucratic staff determined to take charge and compel obedience. 

Resistance to Dutch Rule

To maximize its profi ts, the Company had sought to monopolize trade in those items 

in which it specialized — spices in the fi rst instance, but also textiles, coffee, and tea, 

as the years progressed. Although the rural peasantry may have suffered exploitation, 

their masters, the various Muslim and Hindu/Buddhist aristocracies that ruled them, 

profi ted from their relationship with the Company. The new Dutch government 
20

administration, however, introduced new concepts — cash crops and taxation — that, 

although they maximized profi ts for Holland, tended to circumvent the aristocracy and 

oppress the peasantry. Moreover, it created a fi rm determination to organize economic 

production around a centrally-controlled system of plantations, headed by Dutch 

administrators. A general preference for relying on imported Chinese labor also had 

the impact of further impoverishing the rural peasantry. Accumulating discontent with 

the new Dutch rule gave rise to a general uprising against it in 1825. The Java War of 

1825 – 1830, as it came to be known, was led by a coalition of the Javanese aristocracy 

(traditional sultans and rajas), but had strong peasant support, and cost an estimated 

200,000 Javanese lives before the Dutch succeeded in containing it by 1830.

The Dutch victory in this war consolidated Dutch rule in Java and paved the way 

for extension of this rule over the remaining islands of the archipelago that were not 

otherwise colonized by another European power.23 Dutch success came as the result 

of building a series of small fortresses across Java, manned by small mobile units, that 

gradually enabled the Dutch to exert direct authority over the entire island. Although in 

the immediate aftermath of the Java War the Dutch authorities retreated somewhat from 

the system of direct rule they were in the process of establishing, over the longer run the 

system of indirect rule they established fairly rapidly evolved into a system of direct rule. 

Under the Dutch governor-general, Java was organized into a number of residencies (the 

fi nal number was 16), each of which was administered by a Dutch “resident.” Beneath 

each of the residents, the jurisdiction under his control was further divided into a number 

of bupati (regencies). At this level, the government was confi ded to a Javanese offi cial, 

assisted by a Dutch “advisor,” conceptualized at fi rst as a “younger brother” of the bupati, 

but over time the actual representative of the resident for whom both were employed.

Like the British on the Malay peninsula, the Dutch at fi rst recognized and sought 

to take advantage of the native authority invested in the traditional sultans and rajas of 

Java. Whether the bupati were reigning sultans or not, those whom the Dutch appointed 

to positions of responsibility and authority were drawn from what came to be known as 

the priyayi (aristocratic) class, the families of the sultans and rajas, a class of families 

whose status in Indonesian society was rooted both in royal descent and government 

service. The dominant aristocracy, however, was the Dutch governing establishment 

whose purpose was to organize Java economically in order to derive maximum profi ts 

for the home government.

The Cultivation System

The “Cultivation System,” adopted by governor-general Johannes van den Bosch 

in 1830, a highly centralized economic system that sought to set aside one-fi fth of the 

23 During this period (1820 – 1837), the Dutch were also involved in the Padri War in the Aceh district of 

western Sumatra. This was less an uprising against the Dutch than Dutch involvement in a dispute between 

local religious leaders. The Dutch role in this confl ict drew that nation more deeply into the internal affairs 

of Sumatra than heretofore had been the case.
21

land as plantations producing designated cash crops for export solely for the benefi t 

of the Dutch treasury, was the mechanism for achieving this end.24 Although designed 

to leave 80 percent of the land in the hands of the native Malay rulers, the placing of 

responsibility for returning one-fi fth of their predetermined annual revenues, regardless 

of harvest yield, to the Dutch authorities, in the hands of the bupati administrators, 

had the long-term impact of subordinating the priyayi class, while impoverishing the 

peasantry. Under pressure of the Cultivation System, the former ruling class of Java was 

gradually turned into a salaried bureaucratic aristocracy. The only exception was the 

Sultanate of Jogjakarta (central Java) that continues to this day.

The Liberal Policy

Despite the benefi t to the home government, a liberal Dutch administration in 

1870 began to dismantle the Cultivation System in favor of what was called the 

“Liberal Policy.” Up to this point, all crops had been shipped to Holland by the 

Netherlands Trading Company (NHM), which held a monopoly on the Cultivation 

System. The new policy enabled and empowered other European investors to 

acquire land under long-term leasehold. The policy had the impact of returning 

capital to the Dutch East Indies, rather than solely extracting it. Another impact 

was the gradual conversion of products exported from rice, coffee, sugar, tea, 

and tobacco to new industrial raw materials, such as rubber, copra, tin, and 

petroleum. Yet another feature of the new economic system was increased interest 

in the other islands of the archipelago, so that rapid economic development was 

accompanied by increased territorial expansion. A new legal instrument — the Short 

24 Between 1840 and 1880, revenues from the Dutch East Indies (about 18 million guldens per annum) 

constituted approximately one-third of the annual Dutch budget.

Sultan’s palace in Jogjakarta, Java, Indonesia, September 2000.

Source: NGA Research Center — Ground Photography Collection.
22

Declaration — imposed on local rulers the requirement of accepting the authority 

of Batavia. In this way, by 1910 Dutch authority had been extended over all of 

those territories that were eventually to become Indonesia. New communications 

systems — roads and railways in Java and Sumatra, and regular seaborne shipping 

services-linked Java to the more remote islands of the archipelago. 

The Ethical Policy

The success of the Liberal Policy in organizing a more modern economic sector, 

as it did in the Malayan peninsula, primarily benefi ted the immigrant community, 

mainly European and Chinese, but did little to alter the traditional, largely subsistence 

economy of wet-rice cultivation that characterized the local Indonesian economy. The 

vast gap between these two sectors of the Dutch East Indies led some to advocate 

a more “ethical” policy toward the native inhabitants of the Dutch colony. A new 

liberal Dutch government beginning in 1901 embarked on just such a path, which it 

called the “Ethical Policy.” The aim of the policy was to divert some of the wealth 

generated by the profi table colony back into improved health services, education, 

and agricultural extension work designed to strengthen and modernize the village 

economy. Another aspect of the policy was to provide incentives for inhabitants of 

relatively overpopulated Java to migrate and take up residence on other, relatively 

underpopulated islands of the archipelago. This policy, which continued to be carried 

on by independent Indonesia after 1945, was in effect a Javanese colonization of 

the archipelago, designed to facilitate both economic and political expansion of the 

government in Batavia.

Despite its good intentions, the Ethical Policy achieved little success in terms 

of its stated aims. The agricultural extension programs aimed mainly at improving 

the existing subsistence wet-rice cultivation rather than replacing it and did little 

to diminish the growing gap that was apparent between the traditional and modern 

sectors of Indonesian society. Signifi cant expansion of schools and medical training 

facilities, meanwhile, served mainly the ambitions of the priyayi class who tended 

to be frustrated when, upon graduation, they found their subsequent careers limited 

by “Dutch-only” racial barriers that led some to feel increasingly embittered about 

continuing Dutch rule.

Emergence of Civil Society

Meanwhile, another aspect of the Ethical Policy led to the creation in 1903 of 

representative councils, composed of European, Indonesians and Chinese, in each 

residency, whose function was solely advisory and not legislative; in 1918 of a central 

People’s Council to advise the governor-general in Batavia; and in 1925 of similar 

advisory councils at the bupati level. Designed to buttress the colonial authority rather 

than undermine it, the advisory councils gave a voice to some who sought to infl uence 

Dutch rule on behalf of the native Indonesian populations.
23

Growing opposition to Dutch rule in the early 20th century arose mainly among 

lower members of the priyayi class – low-ranking government employees, impoverished 

aristocrats, schoolteachers, native doctors – most of whom were benefi ciaries of the 

new Ethical Policy but whose ambitions were frustrated by the stronghold maintained 

by the Dutch/upper-priyayi class over the levers of political and economic power. 

Probably facilitated by the Ethical Policy, which encouraged formation of such civil 

society groups, a number of organizations sprang into existence representing a variety 

of perspectives. All sources agree that the fi rst of these was Budi Utomo (Noble 

Endeavor), established in 1908 among students of the School for Training Native 

Doctors in Batavia. Of interest was the decision of this Javanese organization to adopt 

Malay, the lingua franca of the archipelago, rather than Javanese as its language of 

discussion, implying a commitment to a larger political concept than just Java. A 

minority organization comprised of lower priyari, its appeal was limited, and Budi 

Utomo did not endure long.

Sarekat Islam. Other organizations emerged quickly, however. Among these was 

the Islamic Traders’ Association, established in 1909, in an effort to compete more 

effectively with competition from the close-knit Chinese community. In 1912, this 

organization restructured under the name Sarekat Islam (Islamic Union) with the goal 

of becoming a mass organization. Under the leadership of a former priyayi offi cial of the 

Dutch government, Haji Umar Said Cokroaminoto, who cast himself as a charismatic, 

if not divine, fi gure, Sarekat Islam quickly grew into an organization claiming 360,000 

members with some 80 branches throughout the archipelago by 1914. Committed to 

Islamic teaching as well as general Muslim prosperity, the organization also gained 

membership because of a decidedly anti-Chinese appeal.25

The Indies Party. Yet another political movement established in 1910 was the Indies 

Party that advocated an “Indies nationalism” and self-government for the people of 

the Indies in place of the foreign Dutch rule. Led by a mixed-blood Eurasian named 

Dowes Dekker (he took the name Danudirja Setyabuddhi in 1946 after Indonesian 

independence), his more radical activities led to his exile in Holland in 1913 along with 

a few of his associates, and the end of his party. In Holland, however, he associated 

himself during the early 1920s with an organization, the Indonesian Alliance of 

Students, which advocated the same principles.

Muhammadiyah. Still another Muslim group organized in 1912 was the 

Muhammadiyah. Although established in Jogjakarta, it had its early strength in 

Sumatra, where one of its leaders, Muhammad Hatta (later a close associate of 

revolutionary leader Sukarno), had his roots. The Muhammadiyah represented the 

modernist or reformist trend in Islam that sought to implement the very infl uential 

ideas of the Egyptian scholar Muhammad Abduh (d. 1905) and his disciple Rashid 

25 Pearn, Introduction to the History of South-East Asia, 202 – 205. Future revolutionary leader Ahmad 

Sukarno, a Muslim native of Bali, grew up in the home of Haji Umar Said Cokroaminoto and was strongly 

infl uenced by his example and by the model of Sarekat Islam.
24

Rida (d. 1935), the principal publicist of the former’s concepts through his Arabic 

journal al-Manar (Lighthouse). As elsewhere in the Islamic world, where this 

powerful strain of thought was infl uential, the reformist movement was based on 

four major ideas (as adapted for the Dutch East Indies): 

The development of a modern and sophisticated understanding of Islam that 

was in harmony with the principles of Western science and material progress,

The purifi cation of Islamic practice, such as the elimination of animist and 

Hindu/Buddhist elements of Javanese culture that were at variance with Islamic 

teachings,

The encouragement of piety and a serious attitude to the carrying out of religious 

obligations, and

The provision of social services to the Muslim community that the Dutch were 

unwilling to provide.

Other aspects of the Egyptian reform movement were reopening “the gates of 

ijtihad (rational, independent thinking about the Qur’an and hadith) and abandonment 

of taqlid (uncritical acceptance of established, traditional interpretation about the 

Qu’ran and hadith as delineated by the four orthodox madhhab, or schools of Islamic 

jurisprudence, in Islam, and the Shafi ’i school in particular, which predominates in 

southeast Asia). Among other things, the modernist movement advocated the training 

of a new, modern `ulama educated in the principles of scientifi c modernism and a 

progressive understanding of Islam.

Like the Muslim Brotherhood in Egypt (established in 1928 on the same principles), 

the Muhammadiyah organized itself as primarily a philanthropic organization 

supporting a network of modern schools and other institutions such as orphanages 

and hospitals. The sectors of the population from which its membership was 

primarily drawn was the lower middle classes of small and medium-sized towns 

and cities, merchants and, increasingly later, white-collar professionals, clerks, and 

civil servants.26 Adherents of the Muhammadiyah way were generally called santri

Muslims, as opposed to the more syncretic abhangen Muslims.

Communist Party. The year 1914 also saw the formation of the Indies SocialDemocratic Association (ISDV), which in 1920 became the Communist Association 

of the Indies and in 1924 the Indonesian Communist Party (PKI). Active among trade 

unionists and rural villagers and strongly backed by the Communist International in 

Moscow, the party contributed to its own undoing in 1926 – 27 by instigating rural 

uprisings in Java and Sumatra. The government crackdown against the party caused 

it to nearly disappear and not to reappear until the years after independence.

26 Greg Barton, “Islam and Politics in the New Indonesia,” in Jason F. Isaacson and Colin Rubenstein, 

eds., Islam in Asia: Changing Political Realities (New Brunswick, NJ: Transaction Publishers, 2002), 6.

1.

2.

3.

4.
25

Nahdlatul Ulama. In 1926, yet another mass Islamic organization came into being. 

This was the Nahdlatul Ulama (renaissance of the Ulama), established by leading 

traditional `ulama in east Java. The appearance in 1912 of the Muhammadiyah, 

which was highly critical of the practice and teaching of the traditional `ulama, 

had not immediately appeared threatening to them, but over time it did, and the 

Nahdlatul Ulama was their reaction. A goal of the new organization was to defend the 

traditional practices of Indonesian Muslims (generally called abhangen – Muslims 

continuing to practice pre-Islamic rituals, as opposed to santri – Muslims opposed 

to such practices), such as praying at the tombs of men considered to be saints and 

invoking the blessing of one’s ancestors, which the Muhammadiyah scorned as being 

un-Islamic. The abhangen `ulama felt scorned by the arrogant attitude displayed by 

many of the santri toward them. Moreover, the new and more modern schools being 

operated by the Muhammadiyah held the potential for making obsolete the traditional 

pesantren (traditional Islam boarding schools) that were run by the abhangen `ulama. 

In an effort to facilitate networking and cooperation among the traditional `ulama

and their pesantren, this new organization sought to defend the traditional values of 

Indonesian Islam. Although the rural-based NU always remained a looser and less 

homogeneous organization than the more urban-based Muhammadiyah, it too quickly 

enjoyed rapid growth and participation and became much the larger organization. 

Nationalist Party. The most signifi cant of these new organizations over the longer 

term, however, was the Indonesian Union, established in 1927 and soon converted 

into the Indonesian Nationalist Party (PNI) the following year. Founded by a group of 

graduates of the technical college at Bandung, this movement strongly refl ected the 

imprint of its fi rst leader, Ahmad Sukarno, a Balinesian-born Muslim who became 

independent Indonesia’s fi rst president in 1945. The party’s appeal, like that of 

Sukarno himself, was its ability to attract elements of all sectors of Indonesian society. 

Modernist, traditionalist, religious, secularist, Islamic and Marxist all at the same time, 

Sukarno’s party was fi rst and foremost a nationalist party in a land where no strong 

sense of nationhood existed, but for which the cause of independence and self-rule, it 

was argued, transcended the great diversity of Indonesian society. The rapid success 

of the party in recruiting membership, its non-cooperation with the Dutch East Indies 

government, and its declared determination to send the Dutch authorities home as soon 

as possible made it a threat to the Dutch authorities, and in 1929 and again in 1933 

Sukarno and a number of his colleagues were arrested, tried, convicted, and sentenced 

to periods of exile. Without their leadership, the party foundered but did not die. Its 

strength was in eclipse, however, at the time of the March 1942 Japanese occupation 

of the Dutch East Indies during World War II.

World War II

As was the case in the Malay peninsula, the Japanese occupiers deposed and interned 

the previous European colonial government and hired many native Indonesians to 

assist them in running their own administration. Also similar to their policy on the 
26

Malay peninsula, the Japanese cultivated the opponents of Dutch rule. These included 

PNI leader Sukarno and Muhammadiyah leader Muhammad Hatta, both of whom held 

signifi cant positions in the occupation authority and proved to be true collaborators 

with the Japanese.27 Both played this role, however, in the longer-term interest of 

achieving Indonesian independence. Accordingly, in August 1945, on the eve of 

Japanese surrender to the United States, the two men were summoned by the Japanese 

authorities in Saigon, Vietnam, and informed of Japan’s intent to transfer power to 

them. Returning to Jakarta (Batavia), Sukarno, waiting a few days until offi cially 

informed of the Japanese surrender, proclaimed Indonesian independence on August 

17, 1945.

War for Independence

Recognition of Indonesian independence was not obtained solely by declaring 

it, however. Holland was determined to reclaim its colony but, devastated itself by 

its own Nazi occupation during World War II, required help to do so. As they had 

during the Napoleonic wars 130 years before, British troops were dispatched to 

disarm and repatriate remaining Japanese troops on the islands, liberate Europeans 

held in internment camps, and maintain general law and order. The fi rst two tasks 

were accomplished without great diffi culty, but the third proved more diffi cult. Fearful 

that the ultimate British goal was to restore Dutch rule, Sukarno and Hatta moved 

quickly to consolidate their leadership and to organize forces capable of meeting the 

challenge to Indonesian independence. Two institutions started during the war under 

Japanese auspices were transformed into a makeshift government. The fi rst, a 135-man 

committee (BPUPKI) established in March 1945 to begin drawing up a constitution, 

was transformed into the Central Indonesian National Committee (KNIP) that began 

the process of administering the country. The second, a paramilitary organization 

raised by the Japanese, called the Sukarela Tentara Pembela Tanah Air (PETA)—today 

considered the forerunner organization of the Indonesian Armed Forces (ABRI, later 

TNI)—was rallied to defend Indonesian independence.

In the tense situation that emerged, law and order tended to break down and 

legitimate revolutionary activities became diffi cult to discern from other acts of 

criminal violence. Youthful gangs (pemuda) emerged that threatened Dutch settlers 

and members of the old priyayi elite that had collaborated with either the Dutch or 

the Japanese. Dutch armed groups, meanwhile, mobilized to defend their lives and 

their properties and to attack supporters of the new Indonesian government. Clashes 

between santri and abhangen groups occurred, and groups with separatist or leftist 

agendas, contrary to the objectives of Sukarno’s government, proliferated. Although 

it required nearly a decade for Sukarno to bring order out of this growing chaos, the 

event that guaranteed it would be him rather than the Dutch or British who would play 

this role occurred soon after his declaration of independence.

27 Pearn, Introduction to the History of South-East Asia, 213-215, 218-219.
27

This was the Battle of Surabaya (October 24 – November 24, 1945) in Java. British 

troops clashing with pemuda animated by the cause of jihad suffered a signifi cant 

military disaster in which their commander and hundreds of troops were killed. 

British Indian Army troops attempting to retake Surabaya on November 20 – 24 found 

themselves attacked by both PETA forces and thousands of jihad-inspired pemuda. 

Sukarno and Hatta fl ew in to try to halt a massacre of the outnumbered British troops, 

but the battle was not ended until a division of British troops landed, supported 

by naval and aerial bombardments. Unwilling or unable to carry the battle further 

and preoccupied with the problem of reestablishing its own position on the Malay 

peninsula, Britain reached the conclusion that Holland had no choice but to negotiate 

an agreement with the new Indonesian government.

In 1947 and early 1948, a major insertion of new Dutch forces throughout the 

archipelago, coupled with a blockade uneasily supported by the Western powers, left 

the nationalists on the verge of defeat, their territory reduced to roughly a third of Java 

by the time the UN was able to arrange a cease-fi re. By mid-1948, Sukarno and other 

senior leaders had been arrested and sent into internal exile on Sumatra.28

Despite military successes, the Dutch were losing their grip on the East Indies. 

Suppressing the insurgency was costing the Dutch over $1 million a day which they 

could ill afford. The patience of their allies, especially the United States, was also 

growing thin. When the Dutch arrested the nationalist leadership in 1948, the UN 

28 Robert B. Asprey, War in the Shadows: The Guerrilla in History, Vol II (Garden City, NY: Doubleday 

& Co., 1975), 760 – 765.

Typical interior room at the Sultan’s palace, in Yogyakarta, Java, Indonesia, September 2000.

Source: NGA Research Center — Ground Photography Collection.
28

Security Council demanded an immediate cease-fi re and the release of the republican 

leaders, and was backed up by a Truman Administration threat to halt Marshall Plan 

aid to the Netherlands if they failed to comply. Meanwhile, Indonesia’s ability to fi eld 

an army and organize its population was maturing. Facing economic collapse and 

abandonment by their allies, the Dutch agreed to new negotiations in April 1949 that 

culminated in a grant of independence in December.29

A Fragile Independence

The December 1949 grant of sovereignty by the Netherlands established a federal 

United States of Indonesia, of which the Sukarno regime on Java was but one of 

sixteen political units. Once Dutch forces withdrew, this federal system was quickly 

reorganized as the unitary Republic of Indonesia in 1950. The new government, 

fatigued by four years of war, was soon beset by an unsuccessful revolt by the Darul 

Islam movement in western Java, southern Sulawesi, and Aceh. This revolt sought to 

create an Islamic state with greater representation from the outer islands (especially 

Sulawesi, the Moluccas, and Sumatra), rather than the secular state dominated by 

Sukarno and the Javanese elite surrounding him. The rebels hoped to lure the more 

conservative Hatta (who was from Sumatra) away from Sukarno, but failed in this 

gamble as well as in their military confrontation with Sukarno’s tough, loyal army. The 

Darul Islam was only the fi rst of a series of Islamically-inspired revolts in the outer 

islands that continued throughout the Sukarno years. As Sukarno’s personalist rule 

moved the country further toward the Left and increased the dominance of secularists 

and his Javanese followers, the endemic unrest continued.30

29 Asprey, War in the Shadows, 765 – 767.

30 Pearn, Introduction to the History of South-East Asia, 225 – 227; and Hinton, 54.

30

Map of Malaysia

Source: CIA.
31

CHAPTER 2

ISLAM IN MALAYSIA

The basic question for Malaysia remains to be answered: Can there be an increased 

development of a sense of Islamic identity while still maintaining the delicate communal 

balance that has made Malaysia the thriving nation it is today?

 — Fred Van der Mehden

The major fault line in Malaysian politics, as in Malaysian society, is the country’s 

demographic division between its slight majority of native Malays and other Malaysian 

citizens mainly of Chinese or Indian origin. Viewed another way, the fault line is 

between its majority native Muslim population (Malays and others of Indian/Pakistani/

Bangladeshi origin) and its large non-Muslim minority population, primarily Chinese in 

origin. Still another way to view the fault line is to draw it between more economically 

disadvantaged and class-driven traditional society of Muslim Malays, especially in 

the northern and eastern states of the country, and the far more modern, egalitarian, 

and economically developed, largely non-Malay sector of society, especially in the 

western and southern parts of the country. Although one must beware of drawing these 

categorizations too monolithically (there are rich Malays as well as impoverished 

Chinese), they do form the basis of the fundamental political debate that characterizes 

Malaysian society.

ESTABLISHMENT OF MALAY HEGEMONY

In a very real sense, the late 1940s confl ict over the Malayan Union and the ultimately 

victorious Federation of Malaya concepts of how the future Malay peninsula should be 

organized represented a civil war over this fault line in which the traditional Muslim 

Malay sector emerged as dominant. In part this was due to British military intervention 

against the insurgents organized and led by the Chinese-based Malay Communist Party 

(CPM) that proved to be the most diehard champion of the National Union.

Credit also should be given to the United Malay National Organization (UMNO) 

that Malay leaders brought into being in 1946 to protect and advance Malay interests 

and to defend the Federation as opposed to the Union concept. Emerging as Malaysia’s 

dominant political party from that time till the present, its leadership historically kept 

the focus on Malay national rather than Islamic political interests and in general on 

the economic development of the country. Fundamentally a conservative party that 

kept its focus on the secular interests of all, it proved able to reach across Malaysia’s 

ethnic and sectarian divisions and to form alliances with counterpart parties among the 

Chinese and Indian communities. Together, the UMNO, the MCA (Malaysian Chinese 

Association), and the MIC (Malaysian Indian Congress) have been able to dominate 

Malaysia politically throughout its history. As a result, despite many undercurrents of 

division and potential confl icts, Malaysia has remained a relatively stable, democratic, 
32

constitutionally based, parliamentary state that has experienced rapid economic 

development and signifi cant national prosperity.

Undercurrents of Dissatisfaction

The fi ssures in Malaysian society erupted in large-scale rioting in Kuala Lumpur, 

however, over a two-week period in May 1969. The unanticipated violence followed 

national elections in which the UMNO/MCA/MIC alliance failed to secure a 

parliamentary majority (the alliance received 49.1 percent of the vote). Jubilant 

supporters of the opposition parties, mainly Chinese, took to the streets in celebration. 

Accused of taunting onlooking Malays with racial epithets, the celebrants were set 

upon. Although confi ned mainly to the nation’s capital, the communal violence could 

not be ended for two weeks and resulted in hundreds of casualties, mainly Chinese 

and Indians.

The Kuala Lumpur riots of May 1969 proved to be a wake-up call to Malaysia’s 

ruling establishment and a watershed in the country’s modern history. As a result, the 

government set in motion a number of reforms, and various societal reactions also 

occurred. Among the steps taken by the ruling UMNO were a declaration of a state of 

emergency (which has never been offi cially lifted), a suspension of parliament for nearly 

two years, temporary administration of the country by a specially established National 

Operations Council (NOC), and amendment of the Sedition Act of 1948 (created by 

the British to deal with the communist insurgency) to prohibit public questioning of 

the special status of Malays or of Islam, the powers of the Malay sultans, the status of 

Malay as the national language, and the laws of citizenship, particularly with reference 

to non-Malays. With the reconvening of parliament in 1972, the latter provisions of 

the Sedition Act were formally written into the Constitution. Politically, the UMNO, 

aware of its diminished strength as demonstrated in the 1969 elections, embarked on 

a campaign to form alliances with a greater number of political parties than just the 

MCA and MIC. The result in 1974 was the establishment of the Barisan Nasional

(National Front), a coalition of ten parties, headed by the UMNO that has successfully 

dominated national elections since that time.

The Malay Response: The New Economic Policy

Although the riots could have been interpreted as highlighting a need to promote 

greater political equality in Malaysian society, the UMNO-dominated government 

that sought to promote stability by strengthening its own hand politically concluded 

otherwise. The causes of the May 1969 violence were attributed mainly to the 

grievances and frustrations of the Malay element of society that were primarily 

economic in nature. The solution was found in the adoption of the New Economic 

Policy (NEP), promulgated in 1971, that sought to address these grievances by pursuing 

policies favorable to Malay economic interests.Statistics indicated that in 1969 the 

Malay share of national corporate wealth was 2.3 percent, whereas the Chinese share 
33

was 34.3 percent as opposed to the 63.3 percent that belonged to foreign (primarily 

British) owners.31 The NEP was a long-term, 20-year plan that spanned four fi ve-year 

plans, ending in 1990. The stated goal was two-fold-to end poverty in the country, 

which affected mainly Malays who constituted the largest number of poor — and to 

strengthen the Malay share of the national wealth of the country through powerful 

affi rmative action programs discriminating in their favor. The goal by 1990 was for 

Malays to own 30 percent of the national wealth (24 percent had been reached by 

2003), Chinese 40 percent, and foreign owners 30 percent.32 The heart of the program 

was a series of massive public expenditure programs directed mainly at rural Malays 

aimed generally at urbanizing them.33 Among these programs was an ambitious one 

to gradually buy out foreign interests whose shares were sold on favorable terms to 

Malay entrepreneurial investors.34

Although the NEP fell short of its originally stated goals, its overall impact on 

Malaysian society for the next three decades was profound. For the next twentyfi ve years, until the general Asian economic crisis in 1997, the already partially 

modernized economy grew at an unprecedented rate of an average 7 percent per 

year — 8 percent per annum between 1985 and 1995 — making Malaysia one of the 

most prosperous nations in southeast Asia. Previously based primarily on plantation 

and mining activities, with rubber and tin being the principal exports, under the NEP 

the Malaysian economy underwent a great diversifi cation that reduced its dependence 

on overseas commodities markets. Palm oil, tropical hardwoods, petroleum, natural 

gas, and manufactured items, particularly electronics and semiconductors, but also its 

own Proton Saga automobile, were all added to the list of Malaysian exports.

Social Impacts of the NEP

More telling, however, was the social transformation produced by the NEP. In 

order to prepare Malays for the enhanced role they were being empowered to play 

in Malaysia’s economy, under the NEP a number of new scientifi c, technical, and 

vocational schools were established as well as middle schools and four universities, in 

all of which Malays were given preferential admission quotas. Whereas in 1965 only 

21 percent of enrollment in the country’s single University of Malaya were Malays, by 

1977 three-quarters of all students admitted to the country’s now fi ve universities were 

31 Zachary Abuza, Militant Islam in Southeast Asia: Crucible of Terror (Boulder, CO: Lynn Reinner 

Publishers, 2003), 50. Frederica M. Bunge, ed. Malaysia: A Country Study, 4th edition. HQ, Department of 

the Army, DA PAM 550-45 (Washington, DC: U.S. Government Printing Offi ce, 1985), 147.

32 By 1990, the relative share had changed to 20.3 percent for Malays, 46 percent for Chinese and Indian, 

and 35 percent for foreign ownership. The Far East and Australasia, 2003 (London and New York: Europa 

Publications, 2003), 787.

33 Malaysia: A Country Study, 63 – 64. A.B. Shamsul, “Bureaucratic Management of Identity in a 

Modern State: ‘Malayness’ in Postwar Malaysia,” in Dru C. Gladney, ed., Making Majorities: Constituting 

the Nation in Japan, Korea, China, Malaysia, Fiji, Turkey, and the United States (Stanford, CA: Stanford 

University Press, 1998), 145.

34 Malaysia: A Country Study, 144 – 148.
34

Malay.35 Many other Malay as well as Chinese students were sent abroad to secure 

advanced education, Australia being a favored venue for many.

GROWTH OF THE ISLAMIC MOVEMENT

Closely associated with this vast educational expansion was a youth movement, 

especially among Malays, that was perhaps the counterpart of those counter-cultural 

youth movements that fl ourished in many countries during the 1970s — in the late 

and post-Vietnam war eras. In the case of Malaysia, the movement took the form 

of increased interest in religion, or perhaps better to say, the Islamic component of 

the Malay identity. Although empowered by the ruling establishment, the movement 

had a clear anti-establishment cast, identifi ed with opposition to the American role in 

Vietnam and to imperialism in general, and tended to fi nd meaning and enthusiasm 

in the rediscovery of Islam. Many movements emerged, but three in particular have 

garnered the most attention. 

Jamaat Tabligh

The fi rst was Jamaat Tabligh, an Indian-based missionary movement (dakwah

in Malay, dawa’ in Arabic) that had been established in India in the 1920s, came 

to Malaysia during the 1950s to conduct its work primarily in the Indian Muslim 

community, but in the 1970s found its appeal increasingly popular in Malay village 

communities and youth in general.36 Self-consciously apolitical, Jamaat Tabligh

missionaries placed emphasis on personal morality, piety, and strict observance of the 

ritual requirements of Islam. This implied eating and dressing in an “Arabic” fashion 

in imitation of what was believed to be the Prophet Muhammad’s style, characteristics 

that separated the youthful adherents from their Malay elders. Mosque-based in its 

operations, Jamaat Tabligh groups either built or took over existing mosques that 

became centers of worship and further missionary activity. Simple and inoffensive 

in its approach, the movement was not perceived to be threatening and was at least 

tolerated if not actually encouraged by Malaysian authorities.

Darul Arqam

Yet a second was the Darul Arqam movement, founded in 1968 by a former Malay 

government schoolteacher and political activist, Ashaari Muhammad. Far more cultic 

than Jamaat Tabligh, Darul Arqam established an Islamic commune on eight acres of 

35 Malaysia: A Country Study, 123.

36 Jomo Kwame Sundaram and Ahmed Shabery Cheek, “The Politics of Malaysia’s Islamic Resurgence,” 

in Third World Quarterly, 10, No. 2 (April 1988), 846. Also Greg Barton, “Islam, Society, Politics and 

Change in Malaysia,” in Islam in Asia: Changing Political Realities, ed. by Jason F. Isaacson and Colin 

Rubinstein (New Brunswick, NJ: Transaction Books, 2002), 104. 
35

land near the village of Sungei Penchala outside Kuala Lumpur. The commune was the 

forerunner of no less then 40 other communities, 200 schools, charitable associations, 

and dispensaries specializing in the “Islamic” rehabilitation of young drug addicts 

established by the organization in Malaysia, Thailand, and Indonesia before its 

suppression for heresy by the Malaysian government in 1994.37 Similar to Jamaat 

Tabligh in the type of lifestyle it demanded of its adepts-Arabic style dress, turbans, 

eating with hands, avoidance of tables, chairs, and televisions — it nevertheless differed 

by requiring them to live in a closed community, separate from the rest of the 

society. Organizational self-sufficiency was a principal goal of Darul Arqam, and 

the production of halal meat and other Islamic goods emerged as a key attribute 

of the group that enabled it to become a successful business enterprise with 

branches throughout southeast Asia.38 At the time of its 1994 suppression it was 

estimated to have around 10,000 members and assets estimated at $120 million.39

Avowedly apolitical, like Jamaat Tabligh, it nevertheless was innately critical of 

the larger society in which it sought to take root. Sharply critical of other Islamic 

movements in Malaysia, which Ashaari Muhammad claimed only theorized, 

shouted slogans, and conducted seminars, Darul Arqam sought to reestablish a 

“true” Islamic community in the here and now through a formal renunciation of the 

larger society in which it lived.40

ABIM

More important in the longer run than either Jamaat Tabligh or Darul Arqam, 

however, was the Malaysian Islamic Youth Movement — Angkatan Belia Islam 

Malaysia (ABIM) that, as it grew and matured, played an increasingly important 

political role in Malaysian society. Formally established in 1971 at the country’s then 

single University of Malaya for the purpose of “building a society that is based on 

the principles of Islam,”41 ABIM experienced rapid growth and claimed membership 

of 40,000 in addition to many other supporters by the early 1980s.42 Receiving its 

strongest support from Malay youth in Malaysia’s burgeoning institutions of higher 

learning in the 1970s, especially in the country’s more highly developed and urbanized 

western states (Negeri Sembilan, Selangor, and Perak), ABIM may have achieved 

success because of its relatively intellectual appeal. Highly critical of groups like 

37 Gilles Kepel, Jihad: The Trail of Political Islam, 92.

38 Barton, “Islam, Society, Politics and Change in Malaysia,” 105.

39 Kepel, Jihad: The Trail of Political Islam, 94.

40 Sundaram and Cheek, “The Politics of Malaysia’s Islamic Resurgence,” 847. Arqam was one of the 

Prophet Muhammad’s companions in Mecca who had assisted him during his night fl ight to Medina in 

622 AD. Like the Takfi r wa Higra movement in Egypt that also made renunciation of the old sinful society 

(takfi r) and emigration (Hijra) to a new place the symbol of their movement, in a similar way Ashaari 

Muhammad invoked the house of Arqam (Darul Arqam) as a symbol of renouncing society and fi nding 

refuge in a safe place. Barton, “Islam, Society, Politics and Change in Malaysia,” 105.

41 Barton, “Islam, Society, Politics and Change in Malaysia,” 111.

42 Daniel Pipes, In the Path of God: Islam and Political Power (New York: Basic Books, Inc., Publishers, 

1983), 251. Malaysia: A Country Study, 213.
36

Jamaat Tabligh and Darul Arqam for focusing on “mindless ritual practices” and 

“unthinking obedience to Shari’a law,” ABIM placed the emphasis on economic 

and social concerns, how to achieve justice in these areas, and how to make Islam 

a vibrant way of life.43 Study groups, seminars, conferences, and other educational 

venues, precisely those activities so sharply criticized by Darul Arqam, were the heart 

of ABIM activity that served to raise the consciousness of members, facilitate dialogue 

among them, and promote a deeper understanding of Islam and issues affecting 

Malaysia.44 Strongly infl uenced by the examples of Jamiyat-i Islami in Pakistan and 

the Ikhwan al-Muslimin (Muslim Brotherhood) of Egypt, both organizations that 

opposed modern secularism and its political manifestation, nationalism, ABIM took a 

strong stand against the UMNO-sponsored National Economic Policy, which it saw as 

an expression of Malay nationalism. Instead, it advocated the gradual transformation 

of all of Malaysia into an Islamic state, governed by the Shari’a which, it argued, was 

inherently and historically multicultural in spirit and aimed at achieving social justice 

for all members of society. Economically, ABIM argued, government policy should be 

aimed at helping the poor in all sectors of society, not just among the Malays.45

Despite an original intention to remain a civil society organization, fundamentally 

aloof from politics, like Jamaat Tabligh and Darul Arqam, ABIM was quickly drawn 

into a political role. In part this was due to the charismatic leadership of Anwar Ibrahim, 

one of ABIM’s founders (he was 25 years of age in 1971) who became its president 

from 1974 to 1982. Whether it was his intention to play a political role or not, his 

leadership of ABIM cast him into the political spotlight, led to his political co-optation 

by Prime Minister Mahathir Mohammed in 1982, and his designation as Mahathir’s 

eventual successor prior to being rudely dropped from favor and transformed into a 

criminal behind bars in 1998. Probably a more profound reason behind ABIM’s ascent 

into political relevance was the successful UMNO co-optation in 1972 of Malaysia’s 

main Islamic opposition party, the Parti Islam seMalaysia (PAS), into the expanded 

10-party Basilan Nasional (National Front) coalition that continued to dominate 

Malaysia politically in the years after the May 1969 riots in Kuala Lumpur. Although 

PAS justifi ed its decision to join the Basilan Nasional on the basis of strengthening 

Malay solidarity in order to implement the NEP, its joining the coalition had the impact 

of removing it from its traditional role of opposition to the UMNO at a time of rapid 

Islamic resurgence in the country. The absence of PAS from its traditional opposition 

role created a vacuum that ABIM was in a position to fi ll.

PAS — The Islamic Party

Although UMNO had dominated Malaysian politics throughout the country’s 

history, it had never gained the support of all Malays. In large part this was because 

it was correctly perceived as representing the Malay aristocratic classes associated 

43 Pipes, In the Path of God, 251.

44 Barton, “Islam, Society, Politics and Change in Malaysia,”113.

45 Pipes, In the Path of God, 251.
37

with the traditional sultans from which its principal leaders were drawn,46 the ruling 

administrative elite of the government whose loyalty it commanded because of its 

patronage, and its willingness to accommodate multiculturalism.47 Established in 1951 

as an opposition Malay party by former members of UMNO’s religious bureau, PAS 

leaders objected to the secular nationalist leanings of UMNO and from the beginning 

articulated their goal of making an Islamic state out of Malaysia.48 Never a particularly 

strong political party at the national level, its strength was rooted in the economically 

disadvantaged, largely Malay-inhabited northern and eastern states, particularly 

Kelantan and Terengganu, over both of which the party gained political control in 

the fi rst country-wide elections in 1959. Dominated by Islamic teachers (`ulama) in 

the traditional pondoks of northern and eastern Malaysia, the administration of which 

became a principal PAS activity, PAS was in many ways analogous to Nahlatul Ulama

in Indonesia.49 That is, it represented the traditional, more folk, Islam of historic 

southeast Asia rather than the more puritan or modernistic Islam of Jamaat Tabligh, 

Darul Arqam, or ABIM that was to come later. At the same time, PAS was more 

chauvinistically Malay than was UMNO, but because it opposed the more secular, 

nationalist approach of UMNO it had no choice but place its stress on the Islamic 

aspect of Malay nationalism.

Islam and the UMNO

Despite its dominance, UMNO exerted great pressure on PAS in the 1960s in an effort 

to eliminate it politically. It succeeded in recapturing control of the state government of 

Terengganu in 1961 and launched an unsuccessful, large-scale campaign to gain control 

of Kelantan from PAS in the fateful elections of 1969 that produced the Kuala Lumpur 

race riots of May of that year. Meanwhile, in 1962 the UMNO-controlled government 

had gravely weakened the Islamic party by arresting its leader, Dr. Burhanuddin alHelmy, and a number of other PAS leaders for alleged solidarity with Indonesian 

President Sukarno in his efforts to undermine the creation of Malaysia.50 Following 

the 1969 race riots and the adoption of the overtly pro-Malay New Economic Policy, 

the UMNO appeared to have realized its objective of eliminating PAS as a political 

competitor by drawing it into the Barisan Nasional coalition in 1972, but this was only 

a temporary reprieve from an Islamically-based opposition. 

46 Malaysia’s fi rst three prime ministers — Tunku Abdul Rahman (1963 – 1970), Tun Abdul Razak 

(1970 – 1976), and Dato Hussein Onn (1976 – 1981) — were all scions of the royal house of Kedah, or in the 

case of Onn married into it. Not until the election of Dr. Mahathir Mohammed, a “commoner” (also from 

Kedah), as head of UMNO and Prime Minister in 1981 was this pattern broken. The choice of the nonaristocratic Mahathir did not eliminate the perception of whom the party represented, however. 

47 Yong Mun Cheong, “The Political Structures of the Independent States,” in Nicholas Tarling, ed., 

The Cambridge History of Southeast Asia, Vol. 2, Part 2, From World War II to the Present (New York: 

Cambridge University Press, 1999), 83.

48 Barton, “Islam, Society, Politics and Change in Malaysia,” 116.

49 Abuza, Militant Islam in Southeast Asia, 52. Barton, “Islam, Society, Politics and Change in Malaysia,” 

117.

50 Sundaram and Cheek, “The Politics of Malaysia’s Islamic Resurgence,” 849.
38

Given the success of the UMNO in co-opting PAS politically, the fl ourishing 

of Islamist movements in Malaysia in the 1970s can only be explained as a social 

phenomenon among young Malays who were increasingly alienated by the social and 

economic changes affecting the country, in part as a result of the energies released by 

the NEP. Although ABIM, Darul-Arqam, Jamaat Tabligh, and other groups like them 

were all civil society movements, the government clearly saw them, especially ABIM, 

as potentially threatening politically. Later, Prime Minister Mahathir Mohammed 

established his reputation in 1974-1976, when, as education minister, he cracked down 

on Islamic activism on the university campuses by placing restraints on free speech 

and assembly and by ordering the arrest of ABIM leader Anwar Ibrahim for organizing 

a demonstration against the government’s lack of attention to rural poverty.51

The arrest of Ibrahim only strengthened the appeal of ABIM among modern 

Malays, however, and transformed Ibrahim into a fi gure of national stature. Even so, 

UMNO appeared to remain in the ascendant by virtue of its defeat of PAS in Kelantan 

state elections in 1977, depriving PAS of political control anywhere in the country. 

The political humiliation of the rural-based PAS, however, marked the beginning of 

a new openness to personalities of the urban-based ABIM, the entry of many of these 

individuals into positions of leadership in PAS, and the gradual transformation of PAS 

into a more modern, less `ulama-centered organization that espoused an even sharper 

critique of the UMNO-dominated government.52

The essence of the ABIM critique was that Islam should be understood not just to 

be the religion of the Malays, but a universal religion whose full implementation as 

the governing principle of the state would be good for all the peoples of Malaysia, 

Muslim or not. Multiracialism and multiculturalism, according to the ABIM argument, 

were characteristic of Islam, and Islam rather than Malay political dominance was the 

key to establishing a stable and prospering Malaysia. An aspect of this argument was 

a sharp critique of the UMNO’s NEP initiatives on the grounds they were based on 

Malay ethnic chauvinism rather than the good of all the people of Malaysia. ABIM, 

which adopted the slogan “Islam as the Solution to the Problems of a Multi-Racial 

Society,” claimed to stand for a broader, more all-encompassing, and modern vision 

of Malaysia’s future than UMNO, which it was gradually linking to the program of 

UMNO’s principal competitor, the PAS.53 Anwar Ibrahim, the charismatic leader of 

ABIM, was the most effective articulator of this view that gained both him and ABIM 

signifi cant favorable attention in the country’s Chinese and Indian communities and 

appeared to position him as a potential future challenger to UMNO’s historic political 

dominance.

51 Abuza, Militant Islam in Southeast Asia, 53.

52 Barton, “Islam, Society, Politics and Change in Malaysia,” 114.

53 Mohammad Abu Bakar, “Islam, Civil Society, and Ethnic Relations in Malaysia,” in Nakamura Mitsuo, 

Sharon Siddique, and Omar Farouk Bajunid, eds., Islam and Civil Society in Southeast Asia (Singapore: 

Institute of Southeast Asian Studies, 2001), 65 – 66.
39

MAHATHIR GOES ISLAMIC

A change in UMNO’s leadership in 1981 in which 

former Prime Minister and Party leader Dato Hussein 

Onn was replaced by Dr. Mahathir Mohammad brought 

a signifi cant change in the way that the ruling party dealt 

with its PAS/ABIM challenge. In March 1982 Mahathir 

shocked the country by announcing that 34-year-old 

ABIM leader Anwar Ibrahim was leaving his organization 

to join UMNO. Ibrahim’s decision was undoubtedly 

affected by intra-ABIM politics in that, coincidentally 

with his decision to joint forces with Mahathir, his ABIM 

colleague and rival, Terengganu-based Hajji Abdul Hadi 

Awang, was named head of PAS.54 Ibrahim explained his 

decision by saying that he was satisfi ed with UMNO’s 

commitment to Islamic values,55 and indeed he was 

right. A part of their agreement was that if Mahathir 

was not prepared to transform Malaysia into an “Islamic 

state,” he was at least prepared to advance a number of 

initiatives to make Malaysia more Islamic in character.56

Islamic Policies

Very quickly after the co-optation of Anwar Ibrahim 

into the UMNO, a number of measures aimed at 

strengthening Islamic values in Malaysian society began 

to be implemented. Among these were the establishment 

of an Islamic bank, the International Islamic University of 

Malaysia (IIUM),57 an Islamic insurance company, a network of Islamic pawn shops, 

a ban on gambling, a ban on the import of beef not slaughtered in accordance with 

Islamic rules, greatly increased Islamic content on radio and television, introduction 

of Arabic script (jawi) into the primary school curriculum, the suspension of the 

government-run meal program in public primary schools during the month of fasting 

(Ramadan), mandatory teaching of Islam both in elementary schools and in institutions 

of higher learning, a ban on smoking in all government offi ces, and training courses on 

54 Barton, “Islam, Society, Politics and Change in Malaysia,” 118. Yet another factor at work at this time 

was the 1979 Iranian revolution, led by Iran’s `ulama, which was quite favorably viewed by the `ulamabased PAS and those ABIM leaders who were joining PAS. This was in contrast with the UMNO and other 

ABIM leaders such as Anwar Ibrahim whose contacts were close with the oil-producing states of Saudi 

Arabia and Kuwait and who intellectually were more in tune with Sunni Islamic movements, such as the 

Jamiyat-i Islami of Pakistan and the Ikhwan al-Muslimeen of Egypt. Barton, “Islam, Society, Politics and 

Change in Malaysia,” 115.

55 Malaysia: A Country Study, 213.

56 Barton, “Islam, Society, Politics and Change in Malaysia,” 118.

57 For details on the IIUM, one can visit the university’s website at http://www.iiu.edu.my/. 

Muslim woman dressed in 

traditional garb, Malacca, 

Malaysia, May 2001.

Source: NGA Research 

Center — Ground 

Photography Collection.
40

Islamic ethics for all government civil servants.58 All of 

these changes had the impact of promoting a more Islamic veneer to the commercially 

vibrant Malaysian society, but more importantly they had the impact of requiring the 

employment of many religious studies graduates whose services were needed to ensure 

that the new Islamic institutions were operating in accordance with the Shari’a.

59

Another impact was the gradual disappearance of ABIM as an organized body gaining 

popular attention by its critiques of government policy and also the virtual eclipse of 

PAS, at least for the moment, as a political opposition movement to the UMNO and 

the Barisan Nasional.

60

Another aspect of the change toward being a more Islamic country was a noticeable 

increase in Malaysia’s interest in its role as a member of the Organization of the 

Islamic Conference (OIC), as opposed to the active roles it had previously played as 

a member of the British Commonwealth and the Non-Aligned Movement (NAM). In 

addition, it also began to lend support to many Muslim movements elsewhere in the 

Islamic world — e.g. the Palestine cause, the Arakanese in Myanmar, the Chechens 

in Russia, and the Bosnians.61

The Comeback of PAS

Although PAS as a potential political alternative to the ruling establishment headed 

by UMNO and Prime Minister Mahathir Mohammed remained in virtual eclipse 

during the 1980s, it began to make a comeback in the 1990s. In part, this was due 

58 Abu Bakar, “Islam, Civil Society, and Ethnic Relations in Malaysia,” 69. Pipes, In the Path of God, 

251. Milne, 53. 

59 Kepel, Jihad: The Trail of Political Islam, 93– 94.

60 Barton, “Islam, Society, Politics and Change in Malaysia,” 116. In the April 1982 general elections in 

which Anwar Ibrahim had joined the UMNO and campaigned for them, PAS strength dropped to only 14.5 

percent of the popular vote. Malaysia: A Country Study, 226.

61 Abuza, Militant Islam in Southeast Asia, 54.

An Islamic mosque in Kota Baru, Kelantan, northern Malaysia, March 2004.

Source: NGA Research Center — Ground Photography Collection.
41

to the increasingly repressive character of the ruling establishment during this same 

period. Always a party that sought near hegemonic political dominance, but especially 

within the Malay community, the UMNO under Mahathir’s leadership exerted even 

greater energy to press its advantage. Among the mechanisms used was selective use 

of the Internal Security Act provision of the state of emergency condition (that had not 

been lifted since its declaration following the 1969 riots) to arrest dissident opponents 

of the ruling regime. In addition, almost monopolistic control of Malaysia’s media 

outlets and the judiciary, fi nancial patronage to manipulate the electoral process, and 

gerrymandering of electoral districts to ensure UMNO and Barisan Nasional control 

of the political process gave Mahathir almost authoritarian control over the political 

system.62 Unable to challenge UMNO on Islamic grounds, PAS leaders, many now 

former ABIM activists, increasingly were able to portray PAS as the liberal (rather 

than the conservative) party in Malay politics that opposed the authoritarianism and 

increasing corruption associated with UMNO and BN rule.

A split within UMNO in 1987 was necessary for the door to open to a revival of PAS 

political fortunes, however. Unable to successfully challenge Mahathir’s leadership of 

UMNO, political rival Tenku Razaleigh Hamza broke away with a number of other 

UMNO deputies in 1988 to form his own party, Semangat 46 (Spirit of [19]46) and 

entered into a coalition with PAS and the Chinese-based Democratic Action Party 

(DAP), the alternative socialist-oriented counterpart of PAS in the Chinese 

community otherwise dominated by UMNO ally, the MCA. Although the new 

coalition was unable to defeat UMNO and the BN in the 1990 general elections, it 

did make serious inroads into its voting strength.63 Moreover, the BN lost control 

of two state governments, Sabah and Kelantan, the latter of which was taken over 

by PAS after an interval of 13 years.

Under the leadership of PAS leader, Nik Aziz Nik Mat, the new PAS government 

of Kelantan moved quickly to adopt the Shari’a as the prevailing law of the state and 

banned gambling, closed nightclubs, restricted the sale of alcohol, and imposed the 

death sentence for apostasy.64 Although PAS had advocated implementation of the 

Shari’a since its establishment in 1951, it had failed to do so when previously in power. 

Now it did so but immediately came into confl ict with the UMNO-dominated federal 

government that enforced its position that no state decision in criminal law would be 

valid without being sustained at the federal level by the courts of the UMNO-controlled 

judiciary system. The death penalty for apostasy, for example, came into confl ict with 

the constitutional provision guaranteeing freedom of religion. This position, however, 

brought the Mahathir government into direct confl ict with the federal constitution that 

assigned all “matters touching on Malay custom and religion” to the traditional sultans 

who continued to serve as hereditary governors of nine of the thirteen Malaysian 

62 Barton, “Islam, Society, Politics and Change in Malaysia,’’ 120 – 132.

63 The BN gained only 53 percent of the votes, as opposed to 71 percent in 1986. Barton, “Islam, Society, 

Politics and Change in Malaysia,” 124 – 125.

 64 Abuza, Militant Islam in Southeast Asia, 54.
42

states. Accordingly, Mahathir embarked on a campaign to undermine these established 

powers and restrict the already diminished authority of the sultans.

Mahathir Strikes Back

Mahathir had actually begun his effort to limit the powers of the hereditary rulers 

as early as 1983, when he proposed a constitutional amendment that would remove 

the requirement of their assent for approval of any legislation at the state level. In part, 

the confl ict over this issue was the basis of his rivalry with Kelantan aristocrat Tenku 

Razaleigh Hamza, who unsuccessfully tried to unseat him as UMNO leader in 1987, 

leading to the formation of the breakaway Semangat 46 political party. Weakened, 

but still victorious in the 1990 elections, Mahathir revived his campaign to eliminate 

the remaining power of the sultans, and the confl ict with Kelantan state provided the 

venue for doing so. Orchestrating a vicious campaign of innuendo against the personal 

qualities of many of the sultans in the UMNO-controlled media, the UMNO leadership 

subtlely prepared public opinion and undermined popular support for them as much as 

possible. In a series of measures, Mahathir succeeded in adopting a “code of conduct” 

for the sultans, which forbade them from being involved in politics, and in rescinding 

a historic law requiring government offi cials to accord special treatment to them. 

Finally, in May 1994, he was able to obtain approval in the House of Representatives 

for a constitutional amendment that decisively eliminated the power of the sultans to 

block legislation by withholding assent.65

Despite the outrage provoked in the traditional sectors of Malay society by these 

measures, the UMNO/BN coalition won its largest election victory in the history of 

the country in the 1995 elections. In large part the incumbent regime’s popularity was 

due to the phenomenal economic growth most of the country had been experiencing 

for more than two decades, but especially in the early 1990s. In the large Chinese 

community, moreover, the move to adopt Shari’a was perceived as threatening, 

even though the number of Chinese in Kelantan state was very small. The election 

augmented UMNO’s and Mahathir’s powers even more completely, and in September 

1997 he continued his attack on state powers by convening a conference to promote 

the centralization of the administration of the Shari’a, historically and constitutionally 

a state matter, into the hands of the federal government.66

IMPACT OF THE ASIAN FINANCIAL CRISIS

It was just at this moment, however, that Malaysia was hit by the Asian fi nancial 

crisis of 1997. In mid-July 1997 the [Malaysian] ringgit began to depreciate, placing 

sudden pressure on the many fi rms and investors who had borrowed in foreign currency, 

making foreign credits suddenly much more diffi cult to obtain. The Malaysian crisis 

65 The Far East and Australasia, 2003, 766 – 767.

66 The Far East and Australasia, 2003, 767.
43

was precipitated by simple contagion from events in Thailand, but the markets soon 

focused on what were seen as structural problems in the Malaysian system, notably 

overexpenditure on prestige infrastructure projects and opacity in the economy, partly 

as a result of corruption, partly a result of the formal policy of promoting the economic 

development of the Malay community. The ringgit’s decline became catastrophic in 

October, when it lost 40 percent of its previous value within a month.67

The economic crisis provoked a political crisis within Malaysia, particularly 

between Mahathir and his deputy prime minister and fi nance minister, Anwar Ibrahim. 

Whereas Ibrahim viewed the crisis more in domestic terms and argued that ineffi cient 

companies subsidized by the government under the NEP should be allowed to fail, 

Mahathir instead perceived the crisis as resulting from an international conspiracy 

aimed at compromising Malaysian independence. In addition, Ibrahim favored 

strong anti-corruption measures in order to restore international confi dence, a stance 

that placed him at odds with a number of UMNO tycoons. Although both agreed 

that austerity measures were necessary, it became apparent that the two differed on 

where cost cutting should occur. In the end, Mahathir implemented cost reductions 

mainly by reducing government salaries, while preserving as much as he could of his 

government’s grandiose infrastructure projects in which the fortunes of friends and 

relatives was at stake.

The Firing of Anwar Ibrahim

Long considered Mahathir’s natural and designated successor when the former 

retired from offi ce, former ABIM leader Anwar Ibrahim unwisely, but probably 

with integrity, stood in opposition to his mentor, a stance Mahathir, probably also 

unwisely, clearly perceived as being a move to accelerate the political transition 

process. The recent abrupt collapse of the Suharto regime in neighboring Indonesia in 

May 1998, due to popular pressures brought on by the Asian fi nancial collapse, may 

also have been a factor infl uencing both men. Accordingly, in early September 1998 

Mahathir again shocked the nation by suddenly announcing Ibrahim’s dismissal from 

all his government positions and from membership in UMNO. Despite the storm of 

controversy provoked by this precipitous action, the storm only deepened, when three 

weeks later Ibrahim was abruptly arrested and charged with several clearly trumped-up 

counts of illegal behavior, including corruption. Allegations of police brutality against 

Ibrahim within prison infl amed tensions even more. Throughout his trial, in which the 

court eventually declared him guilty in April 1999 and sentenced him to fi fteen years 

67 The Far East and Australasia, 2003, 767.
44

in prison,68 riot police had to hold at bay large numbers of protestors who maintained 

a more or less permanent vigil.

Politically, Ibrahim had been popular, particularly with Malaysian youth, and his 

association with UMNO had kept many of them loyal to the party. To these, Mahathir’s 

perceived cruel treatment of Ibrahim was emblematic of the autocratic character, 

including total emasculation of the judiciary, of the now long-serving prime minister. 

Following the arrest of Ibrahim and during and after his trial, large numbers of his 

supporters began to defect from UMNO and fl ocked to PAS, quickly reviving the 

main Malay opposition party’s challenge to historic UMNO dominance.69 Aware of 

this relative loss of support, but also taking into account the partial recovery of the 

Malaysian economy by late 1998, Mahathir again surprised the country by advancing 

the date of federal elections from April 2000 to November 1999.

The Price of Victory

Although, as expected, Mahathir and the UMNO continued to dominate Malaysian 

politics in the 1999 elections, PAS and a coalition of allied opposition parties grouped 

into a Barisan Alternatif political front made serious inroads at the expense of the 

Barisan Nasional, leaving UMNO with only 57 percent of the seats in parliament, 

as opposed to the 65 percent the party had controlled since 1995. More importantly, 

PAS regained control of Terengganu state that it had lost, seemingly irrevocably, 

in 1961, and it posed serious challenges to UMNO control in several other, largely 

Malay states (Perlis, Perak, and Kedah-Mahathir’s home state) in the north and east 

of the country. The signifi cance of winning in Terengganu was that, unlike relatively 

impoverished and underdeveloped Kelantan (both having Malay majorities of about 

95 percent), Terengganu had become a signifi cant petroleum and gas-producing state 

in which the sharing of revenues derived from these resources between the federal 

government and the state was a matter of bitter dispute. Soon after the PAS victory, 

Mahathir’s government required that all royalties derived from offshore platforms 

facing Terengganu go to the central treasury, overnight reducing Terengganu’s budget 

by 80 percent. Although the move provoked outrage in Terengganu state and made it 

more diffi cult for PAS to govern effectively, it also made state authorities more highly 

68 Ibrahim was released from prison on September 2, 2004, precisely six years to the day from his 

dismissal from offi ce as deputy prime minister and fi nance minister. The release was ordered by Malaysia’s 

Federal Court, which by a two-to-one vote found the original court decision “fl awed.” Mahathir’s successor 

as Prime Minister, Abdullah Badawi, was said not to have intervened to infl uence the court’s decision. 

Mahathir himself had retired as prime minister in October 2003.

69 Ten months after Ibrahim’s arrest, PAS membership rolls were said to have jumped by 20 percent— to 

120,000. By 2001, PAS claimed to have 800,000 members. In contrast, UMNO membership was said to be 

2.7 million souls. PAS remained a relatively small opposition party; yet the strength of its opposition was 

signifi cantly augmented as a result of the Anwar Ibrahim case. Abuza, Militant Islam in Southeast Asia, 

56 – 57. 
45

dependent on the largess of Kuala Lumpur, and PAS leaders dependent on the good 

will of UMNO leaders to maintain themselves.

MILITANT ISLAM IN MALAYSIA

A feature of Islamic resurgence and growing Islamization in Malaysia in the years 

after 1969 was also the undercurrent of militant Islamic fundamentalism. The dilemma 

of Malay politics has been how the dominant Malay ruling elite can maintain control 

of the country in association with Chinese and Indian elites without alienating the 

support of the Malay majority in the country and also maintain support of a majority of 

Malays without alienating the large and economically signifi cant Chinese and Indian 

communities in the country. Through the years UMNO has effectively balanced the 

inherent tensions in this dilemma by focusing on economic development-centered in 

the Chinese community and by diverting the surplus wealth generated by this economic 

development to help ameliorate the relatively underdeveloped Malay community. The 

more Islamically-oriented PAS, on the other hand, remained a minority party because 

it was a more chauvinistically Malay party that found it diffi cult to gain the trust of a 

suffi cient number of Chinese or Indians (non-Muslims) to be victorious electorally at 

the national level, although it could win in the Malay-majority states in the north and 

east. With the growing Islamization of the ethnic Malay community, which ought to 

have strengthened the appeal of PAS to the ordinary Malay, UMNO could only cope 

with this challenge, or so Mahathir believed, by co-opting the Islamic movement for its, 

and his, own purposes, i.e., to maintain UMNO’s political hegemony over the Islamic 

party within the Malay community (PAS), while maintaining suffi cient support in the 

Chinese and Indian communities to assure UMNO electoral supremacy. Increasingly, 

as Mahathir pursued an Islamization policy, however, his style of leadership was 

forced into what one political scientist has called a “repressive, responsive” approach70

toward governance. Although Malaysia remained a democracy, the ruling party 

increasingly relied on authoritarian methods to maintain its hegemony, while seeking 

to be responsive to the perceived needs and desires of the communities it governed.

Early Incidents

It was in this context that some Malays developed a more militant posture 

toward the ruling regime. The fi rst major instance of a government crackdown on 

Islamic elements apparently inciting violent action against it was in 1984, when the 

Mahathir government took action to imprison a number of PAS youth leaders who, 

infl uenced by the example of the Iranian revolution of 1979, were advocating a similar 

revolution in Malaysia. Then in November 1985, in a second incident, government 

forces surrounded and attacked the village of Memali in the Baling district of Kedah 

state. There, under the leadership of a PAS extremist, Ustaz Ibrahim, the village had 

70 Harold Crouch, Government and Society in Malaysia (Ithaca, NY: Cornell University Press, 236-

247). 
46

been organized into an Islamic commune, perhaps on the model of Darul Arqam, and 

refused to recognize any higher political authority. Well-armed to defend itself, the 

Memali commune evoked a government response remarkably analogous to that of the 

Syrian government in the city of Hamah in February 1982 or the U.S. government to 

the Branch Davidian cult in Waco, Texas, in February 1993. The standoff resulted in 

an attack by government forces, which resulted in the deaths of 14 villagers and four 

policemen as well as the arrest of 160 commune members, including children.71

Lure of the Afghan Jihad

Although data are sparse, it was also during this period — the mid-1980s — that 

recruiters based in Pakistan, probably part of the Peshawar-based Maktab al-Khidmat,

72

(MAK) headed by the Arab professor Abdullah Azzam, began traveling in Southeast 

Asia seeking young Muslim recruits to participate in jihadist activities against the 

Soviet occupation of Afghanistan. Indonesian and Filipino Muslim youth may have 

proved more responsive to these appeals than Malaysians, but Malaysia itself, as 

well as Singapore, soon emerged as major transit points and processing centers for 

individuals from Southeast Asia moving to and from Pakistan and Afghanistan.

There were several reasons for this phenomenon. First, the Malaysian government 

embarked on its own Islamization campaign, and like most Muslim governments, was 

supportive of the Afghan resistance to the Soviet occupation. Secondly, as a relatively 

open society, particularly in comparison to neighboring Indonesia under Suharto or 

the Philippines under Marcos, the traffi cking in persons, money transfers, or arms 

shipments could occur with little monitoring or state concern. Thirdly, as a country 

with a fl ourishing economy, Malaysia had a large requirement for foreign labor. This 

circumstance led the Mahathir government to ease visa restrictions for entry into 

Malaysia, especially for people from Muslim countries, in the decade plus prior to 

the Asian fi nancial crisis of 1997. Finally, most of the work associated with support 

for the Afghan resistance was in the hands of foreign elements in Malaysia-Arabs in 

the fi rst instance, but also increasingly with the passage of time militant Islamic exiles 

mainly from Indonesia. As a result, the recruitment, training, supporting, and sending 

of Southeast Asian youth to Pakistan and Afghanistan was work the government could 

tolerate and even empower; it was not work for which the government had specifi c 

responsibility. Such conditions continued in Malaysia, even after the Soviet withdrawal 

from Afghanistan, and the Maktab al-Khidmat was gradually transformed into a new 

organization called al-Qa'ida.

71 Barton, “Islam, Society, Politics and Change in Malaysia,” 119.

72 Literally Maktab al-Khidmat l’il-Mujahideen al-Arab (Offi ce of Services of the Arab Mujahideen).
47

Jemaah Islamiyah

The specifi c Indonesians involved with and who came to be associated with 

the Malaysian-based (until 1998), al-Qa'ida-linked, pan-Southeast Asian Islamist 

organization, Jemaah Islamiyah (JI), formally established on January 1, 1993,73 had 

mostly come to Malaysia in the mid-1980s, fl eeing the Suharto regime. Although their 

numbers were many,74 of special note were Abdullah Sungkar (1936 – 1999), founder 

and leader of JI, and two key associates, Abu Bakar Ba’asyir (b. 1938) and Muhammad 

Iqbal Rahman (aka Fikiruddin, aka Abu Jibril). Yet another individual, signifi cant for 

the important leadership role he eventually came to play, was a young 20-year-old, 

Riduan Isamuddin (aka Hambali, b. 1966).

Although Hambali may not have been entirely typical of the many who went to 

Pakistan and Afghanistan and returned to Southeast Asia imbued with the jihadist 

spirit, the pattern is typical enough to be used as a paradigm for many of the others 

who followed the same path. Said to have arrived in Malaysia in 1985 in fl ight from 

Indonesia, he is alleged to have had university studies as his primary goal. He was, 

however, recruited to join the jihad in Afghanistan, where he served for an apparent 

three-year period between 1988 and 1990. There he is said to have met and worked 

with Usama bin Ladin, a close associate of Abdullah Azzam, and subsequently the 

latter’s successor following his death in November 1989.

On his return to Malaysia in late 1990 – early 1991, Hambali lived an apparently 

simple life as a roadside kebab seller, butcher, and later as a peddler and itinerant 

preacher. Although he lived in virtual poverty, he made use of his traveling to 

preach, spot recruits, raise funds, and organize travel of recruits being sent either 

to Pakistan or the Philippines.75Among those who traveled to Pakistan at this 

73 Other sources give varying dates for the formal establishment of Jemaah Islamiyah, from 1989 to 

1995. In November 2002, a document found on the computer of Imam Sumudra known as the PUPJI 

document (Constitution of Jemaah Islamiyah) established the founding date of the organization as January 

1, 1993. See below, Chapter 4, 101. I had earlier selected 1992 as refl ecting the historical progress of events, 

as noted in the paragraphs that follow, which indicate that 1992 was the likely date.

74 Abuza gives the number as around 800. Abuza, Militant Islam in Southeast Asia, 125.

75 Biographical data on Hambali are very incomplete. This perspective is based largely on a journalistic 

account: Baradan Kuppusamy, “Hambali: The Driven Man,” from Asia Times Online, 19 August 2003. 

URL: www.atimes.com/atimes/Southeast_Asia?EH19Ae06.html, accessed 2 November 2004. The details in 

this article have been closely cross-checked with other journalistic accounts of Hambali, however.
48

time to meet Usama bin Ladin was Abdullah Sungkar.76 Soon after his return, he, 

Ba’asyir, Fikiruddin, Hambali, and others moved from diverse places of residence 

to the coastal village of Sungei Manggis in southern Malaysia, a ferry ride away 

from Indonesia across the Strait of Malacca. The Jemaah Islamiyah movement, of 

which these men were the central leadership, dates from this gathering at Sungei 

Manggis in early 1992.77

Roots of Jemaah Islamiyah

The concept of jemaah islamiyah was not a new one dating from this moment, 

however. Both Sungkar and Ba’asyir considered themselves the spiritual heirs of 

Sekarmadji Kartosuwirjo — the founder-leader of the Indonesian Darul Islam movement 

in western Java whose struggle to create an “Islamic state” in Indonesia was brutally 

crushed by the Sukarno regime during the 1950s.78 Believing that the Darul Islam

movement had failed because Indonesian society (jemaah) was not yet ready, both 

Sungkar and Ba’asir spoke of the need of a longer-term process to foster the creation of 

a jemaah islamiyah (Islamic society) as a necessary prelude to establishing an Islamic 

state. In furtherance of this goal, and in time-honored Indonesian tradition, the two in 

1972 established an Islamic boarding school (pesantren), called al-Mukmin in Ngruki 

(suburb of Solo). Starting with 30 students, the institution had grown to 1,900 students 

by the year 2000. The later Jemaah Islamiyah organization, founded by Sungkar and 

76 This may have been Sungkar’s second trip out of Malaysia since his arrival in 1985, as well as his fi rst 

meeting with bin Ladin. The exchange must have occurred between April and December 1991, the brief 

period that bin Ladin lived primarily in Peshawar, Pakistan, after his surreptitious departure from Saudi 

Arabia and later decision to settle in Sudan. This brief period, which is virtually ignored in the plethora of 

bin Ladin/al-Qa'ida literature that has appeared since September 2001, may well have been the true starting 

point of al-Qa'ida as an organization striving for global reach. Another visitor to bin Ladin at this time 

was the soon-to-be Filipino Abu Sayyaf leader, Abdurrajak Abubakar Janjalani. Upon the latter’s departure 

from Pakistan in December 1991— the same time as bin Ladin’s departure for Khartoum-Janjalani was 

accompanied by an individual, sent with him by bin Ladin, whom the United States less than two years later 

would know by the name of Ramzi Yousef. The Abu Sayyaf group in the Philippines dates from early 1992, 

following Janjalani’s return home from Pakistan, although bin Ladin had established earlier contact with the 

Filipino Muslims in 1988 when he had sent his brother-in-law, Muhammad Jamal Khalifa, to the Philippines 

to obtain recruits for the war in Afghanistan. Rohan Gunaratna, Inside al-Qaeda: Global Network of Terror 

(New York: Columbia University Press, 2002), 178; Abuza, Militant Islam in Southeast Asia, 92. Unlike 

Sungkar, Janjalani had traveled to Afghanistan before. He was part of an alleged 300 Filipino recruits to 

have been brought to Pakistan in the mid-1980s to participate in the jihad against the Soviet occupation of 

Afghanistan. There is no evidence that Hambali traveled to Pakistan at this time with Sungkar, but in light 

of subsequent events it seems reasonable that he did. The only account dealing at all with this brief period 

of bin Ladin’s stay in Pakistan is that found in Adam Robinson, Bin Ladin: Behind the Mask of the Terrorist

(New York: Arcade Publishing, 2001), 133 – 134. Even this account is virtually devoid of comment on bin 

Ladin’s activities during this period, however.

77 Gunaratna, Inside al-Qaeda, 195.

78 Abuza, Militant Islam in Southeast Asia, 126.
49

Ba’asir in 1992, was to be heavily populated by graduates of this institution.79 Like 

the Muhammadiyah mass organization of Indonesia, the curriculum of al-Mukmin was 

strongly infl uenced by the modernist arguments of Muhammad Abduh and Rashid 

Rida. Unlike the Muhammadiyah, however, Sungkar and Ba’asir placed emphasis on 

the incompatibility of a society that adhered to God’s laws (Shari’a) and the society 

that did not. A true Islamic state could come into being only by a jemaah islamiyah that 

was characterized by strength — strength of faith, strength of brotherhood, and military 

strength — a strength that would enable the faithful society ultimately to crush its 

enemies, as the Darul Islam movement had earlier been crushed in the 1950s. Arrested 

and imprisoned for four years by the Suharto regime for “subversive” activities in 

1978, Sungkar and Ba’asyir fl ed to Malaysia in 1985 on learning they were about to 

be arrested again.80

Objectives of Jemaah Islamiyah

The decision to formally organize a group called Jemaah Islamiyah in Malaysia 

in 1992 – 93 obviously came as a result of meetings with bin Ladin in Peshawar and 

79 See, for instance, the roster of JI activists provided by the Brussels-based International Crisis Group, 

“Indonesia Backgrounder: How the Jemaah Islamiyah Terrorist Network Operates,” from ICG Online, 11 

December 2002. URL: http://www.crisisweb.org/home/index.cfm?id-1397&1-1. Accessed 12 December 

2004.

80 Abuza, Militant Islam in Southeast Asia, 126 – 127. 

Muslim tourists at St. Paul Hill, Malacca, Malaysia, May 2001.

Source: NGA Research Center — Ground Photography Collection.
50

probably also funding from him. The primary focus of the organization, however, 

was not Malaysia, but the use of Malaysia as a convenient and reasonably secure 

transit point for the conduct of operations elsewhere, primarily in the Philippines and 

Indonesia. If the defi nition of a terrorist organization requires that the group fi rst be 

assigned responsibility for an act of terrorism, then JI could not be effectively identifi ed 

as such until August 2000, when it conducted its fi rst-known terrorist operation — the 

assassination of the Philippine ambassador in Jakarta.81 By this time, the leadership 

cadre of JI and many of its other activists had returned to Indonesia, following the 

collapse of the Suharto regime in May 1998. The period of the 1990s was primarily a 

time of organizing, recruiting, training, planning, and developing of the fi nancial and 

logistical infrastructure to support violent actions that would come later and in which 

the Malaysia of Prime Minister Mahathir Mohammed served as a relatively free safehaven for such intrigues. 

The principal operational leaders of this effort appear to have been Hambali and 

another Indonesian, Muhammad Iqbal Rahman (aka Abu Jabril), who served as head of 

training for all JI cadres operating in Southeast Asia.82 Under their leadership, contacts 

were made and JI cells (fi ah) established throughout Southeast Asia for the purposes 

of training and taking responsibility for unique types of operations (arms training, 

explosives manufacture, media activities, etc.). These fi ah, in turn, were grouped 

into four mantiqi: one for peninsular Malaysia, southern Thailand, and Singapore; 

the second for all Indonesia, except for Borneo (Kalimantan, Sabah, Sarawak, and 

Brunei); the third for the Philippines, all Borneo, and Sulawesi in eastern Malaysia; 

and the fourth for Australia and Papua (Irian Jaya). Each of the mantiqi was headed by 

a Hanbali lieutenant.83

Until the departure of the JI leadership to Indonesia in 1998, the Malaysian mantiqi

was the largest part of the growing JI organization as well as its focal point. It was 

here that links were maintained with the al-Qa'ida organization, fi rst in Sudan, but 

later in Afghanistan and Pakistan, and with the fi ghting groups in the Philippines and 

Indonesia. The Malaysian mantiqi was also the fi nancial center of the JI and primary 

meeting place for JI and al-Qa'ida planners. Through the Malaysian mantiqi, which 

also included Singapore, passed the approximately 100 recruits who traveled to 

Pakistan and Afghanistan during this period. Other recruits were sent to the Philippines 

to receive training from al-Qa'ida and other trainers. The Malaysian mantiqi also 

operated its own training camp in Negeri Sembilan.

81 In fact, the existence of Jemaah Islamiyah became known only in December 2001, when a tape detailing 

plans of the Singapore cell was discovered in the home of al-Qa'ida military commander Muhammad Atef 

(Abu Hafs al-Misri) in Kabul, Afghanistan. See below, Chapter 4, 100-101. Jemaah Islamiyah operations 

prior to this date were unattributed.

82 A detailed description of JI organizing activities during this period is provided by Abuza, Militant 

Islam in Southeast Asia, 125 – 140, on which this account is largely based. 

 83 Abuza, Militant Islam in Southeast Asia, 132.
51

Jemaah Islamiyah and al-Qa'ida

Finally, the Malaysian mantiqi also established a number of front companies 

that were used to channel funds from al-Qa'ida as well as to procure weapons 

and materials used in bomb-making. One of these, called the Konsojaya Trading 

Company, established in June 1994 by Hambali, al-Qa'ida operative Wali Khan 

Amin Shah, Afghan investor Mehdat Abdul Salam Shabana, Saudi investor 

Hemaid H.Al-Ghamdi, and four others, appears to have been set up primarily 

to support OPLAN Bojinka in the Philippines — the abortive plan led by New 

York World Trade Center bombing planner, Ramzi Yousef, to assassinate U.S. 

President Clinton and Pope John XXXIII, and to bomb simultaneously 11 U.S. 

aircraft over the Pacific sometime in early 1995.84

Even after the departure of the JI leadership to Indonesia in 1998, the Malaysian 

mantiqi continued to play a central role in coordinating JI and al-Qa'ida operations. 

Key planning for the October 2000 bombing of the American ship USS Cole in the 

port of Aden, as well as the September 11, 2001, aircraft attacks on New York’s World 

84 Gunaratna, Inside al-Qaeda, 195; Abuza, Militant Islam in Southeast Asia, 129.

Sultan’s palace in Kota Baru, Malacca, Malaysia, March 2004.

Source: NGA Research Center — Ground Photography Collection.
52

Trade Center and the Pentagon in Washington, DC, took place under JI cover at a 

meeting in Kuala Lumpur on January 5, 2000.85

The KMM — JI’s Malaysian Counterpart

Although Jemaah Islamiyah emerged on Malaysian soil, it did not attract too many 

Malays. Two small groups of Malaysians were said to have been sent to Pakistan and 

Afghanistan prior to the Soviet withdrawal in 1989. Others followed, but in small 

numbers, during the 1990s. Among those who had the experience of jihad and thus 

could call themselves mujahidin, many continued to carry the legacy with them. Some 

of these,86 along with others, on October 12, 1995, formed a new militant organization 

called the Malaysian Mujahidin Group (Kampulan Mujahidin Malaysia — KMM), under 

the leadership of Afghan veteran Zainon Ismail. The formation of the KMM followed 

the Malaysian elections of 1995 in which Mahathir’s UMNO secured its largest electoral 

victory ever, leaving some associated with the new KMM to abandon hope that a “true” 

Islamic state could ever be established through democratic means, nor that PAS could 

ever win at the national level electorally. Accordingly, KMM established itself as a 

covert organization dedicated to overthrowing the UMNO-led government by force in 

the interest of establishing Malaysia once and for all as an Islamic state.

The precise relationship between KMM and Jemaah Islamiyah is unclear, as was 

the relationship between KMM and PAS. Although KMM was an independent group, 

some of its members also belonged to Jemaah Islamiyah, and most KMM members 

were supporters of PAS, if not members, but were disillusioned by PAS’s continuing 

commitment to work through the democratic process. A key KMM leader, moreover, 

was the son of Kelantan-based PAS leader Nik Aziz Nik Mat-Nik Adli Nik Aziz-the 

latter said to have served six years in Afghanistan between 1990 and 1996.87 Returning 

to teach Arabic in his father’s PAS-operated school in Kelantan’s capital, Kota Baru, 

Nik Adli became increasingly involved with the KMM and allegedly committed to a 

violent overthrow of the Malaysian government. Later charges against him included the 

purchase of a large number of weapons and explosive materials from Thailand in 1999, 

close and continuing contacts with the JI leadership, including Hambali, the dispatching 

85 Among the attendees at the meeting were (1) Khalid al-Mihdar and (2) Nawaf al-Hazmi, two of the 

hijackers who fl ew American Airlines Flight 77 into the Pentagon. Other attendees included (3) Ramzi bin 

al-Shibh of the Hamburg al-Qa'ida cell, a close associate of September 11 leader Muhammad Atta who 

allegedly failed to be a twentieth hijacker because of his inability later to obtain a visa enabling him to enter 

the United States; (4) Khalid Shaikh Muhammad, overall planner of both the USS Cole operation and the 

9/11 operation; (5) Tawfi q bin Atash, an alleged key operative associated with the attack on the USS Cole; 

(6) Fahad al-Quso, the alleged key planner behind the August 1998 bombing of two U.S. embassies in 

East Africa; (7) Ahmad Hikmat Shakir, a key al-Qa'ida operative of Iraqi origin; and (8) Hambali. Abuza, 

Militant Islam in Southeast Asia, 123.

86 Abuza says the number was 45. Abuza, Militant Islam in Southeast Asia, 124.

87 Gunaratna, Inside al-Qaeda, 196.
53

of KMM members to train in MILF camps in the Philippines, and participating in battles 

against Christians in the Maluku Islands (Indonesia), also in 1999 and early 2000.88

Demise of the KMM

The KMM was uncovered during the summer of 2001. A bank robbery in May of 

that year in which police killed two and detained six KMM members led to confessions 

implicating others. Although the KMM leadership may not have authorized its members 

to conduct this crime, they nevertheless were revealed as a result of the failure of the 

bank operation. On August 4, 2001, Zainon Ismail, Nik Adli, and eight other alleged 

members of the KMM (seven of whom were also PAS members) were detained for 

attempting to violently overthrow the Malaysian government and establish an Islamic 

state. The police also linked KMM to a number of other crimes, as enumerated above.89

Following the September 11 attacks on the United States and growing evidence of 

deeper involvement in terrorist activities, many more were arrested. Altogether, 68 

members of KMM were eventually identifi ed and imprisoned under the provisions of 

the all-embracing Internal Security Act of 1948.

A year before, and under similar circumstances, yet another militant group called 

Al-Ma’unah, apparently unconnected to KMM, had been uncovered, when in July 

2000 members of the group had seized weapons from military stockpiles in northern 

Perak State. In the ensuing four-day standoff, two government offi cials were killed 

before the group surrendered. The leader of the group, Mohammed Amin Razali, 

was a Malay who had served too in Afghanistan in the 1980s. Also infl uenced by 

the model of the Indonesian movement of the 1950s but not apparently affi liated 

with Jemaah Islamiyah Darul Islam or its leadership, Razali had returned to Malaysia 

to form his own cult-like group, four of whose members, including himself, were 

sentenced to death on December 27, 2001, for plotting the violent overthrow of the 

Malaysian government.90

88 Some critics of the Mahathir regime argued that the charges against Nik Adli were trumped up as a 

means of discrediting his father and PAS in general. Although PAS continually disclaimed any connection 

with KMM and Nik Aziz did nothing to defend his son, the allegation that UMNO might transform the 

troubles of Nik Adli into political advantage against PAS was credible. Abuza, Militant Islam in Southeast 

Asia, 125.

89 Abuza, Militant Islam in Southeast Asia, 156.

90 Abuza, Militant Islam in Southeast Asia, 125. An editorial in the UMNO-oriented Kuala Lumpur 

New Straits Times interpreted the incident as follows: “[I]t would appear that the Al-Mu’unah movement is 

perhaps a manifestation of an irrational extremism and militancy within PAS itself...In terms of size, it may 

be a small element. Nevertheless, it is a dangerous development, for, as shown by the fanatical actions of 

the Al-Mu’unah members, it imperils national security, bordering on lunacy and threatening to bring about 

the disintegration of Malaysia. Agreed, this development may not have been endorsed or encouraged by 

the PAS leadership. But does it matter? It was from within the larynx of the party’s leadership that the hate 

emanated. As observed by Prime Minister Datuk Seri Dr. Mahathir Mohammad, Al-Mu’unah is the direct 

result of PAS’s campaign of hatred for the Government.” New Straits Times (Internet Version in English), 

July 21, 2000. Document ID SEP20000721000072, accessed on Intelink June 5, 2000.
54

IMPACT OF THE 9/11 ATTACKS ON MALAYSIA

Although the al-Qa'ida-sponsored attacks on the United States on September 

11, 2001, raised the possibility that Malaysia could be identifi ed as a country that 

harbored international terrorists, particularly after it became known that two of the 

aircraft hijackers had resided in Malaysia and attended the January 2000 meeting in 

Kuala Lumpur where at least a part of the planning for the operation had occurred, the 

event in fact proved a political boon to Prime Minister Mahathir Mohammed and the 

UMNO. Mahathir immediately condemned the September 11 attacks and promised 

to fi ght terrorism within Malaysia. He moved quickly to suppress the just discovered 

KMM organization and promised close cooperation with the United States on tracing 

al-Qa'ida fund transfers in Malaysia. He also moved quickly to close down a key alQa'ida website (www.alneda.com) that was hosted on a Kuala Lumpur internet server. 

Close cooperation with the United States brought an invitation for a state visit to 

Washington, DC, in May 2002, the first such visit since 1994, where Mahathir 

signed a formal agreement with U.S. President George W. Bush to cooperate in 

combating terrorism.

While mending and consolidating ties with Washington, Mahathir also preserved his 

credentials as a Malaysian nationalist leader. He publicly rebuffed a formal request from 

the United States to hand over several hundred people on a U.S. list of terrorist suspects, 

stating that he would only do so if “the United States provided direct evidence that they 

had committed a crime within the United States.”91 Terrorists charged with committing 

crimes in Malaysia, he asserted, would be tried in Malaysian courts in accordance with 

Malaysian law.92 He also refl ected the views of many Malays and Muslims around the 

world by strongly criticizing the U.S. military response to the September 11 attacks by 

invading Afghanistan, while failing to make concerted “efforts...to fi nd the reasons why 

these terrorists chose to resort to violence in the fi rst place.”93

Mahathir’s primary political response to the September 11 attacks, however, was 

domestic. He adroitly used the crisis to link PAS in the minds of Malay voters with 

Islamic extremism, terrorism, the KMM, and JI, whose presence in Malaysia and 

its links to al-Qa'ida he fi nally became able to admit. Declaring on September 29, 

2001, that Malaysia was already an Islamic state,94 Mahathir sought to brand PAS 

as Taliban-like extremists who wanted to implement an extremist form of Islam and 

carry Malaysia backward rather than forward in its development.95 Although this 

91 Abuza, Militant Islam in Southeast Asia, 213.

92 On the other hand, an Oregon-based terrorist suspect, Ahmed Ibrahim Bilal, who was found to be 

studying at Malaysia’s International Islamic University, was immediately deported to the United States. 

Abuza, Militant Islam in Southeast Asia, 213.

93 Patrick Senayah, “U.S.-led Bombings of Afghanistan Won’t Resolve Terrorism: Dr. M.” Kuala Lumpur 

New Straits Times, October 14, 2001.

94 Talk given by Patricia Martinez (University of Malaysia) at the U.S. Department of State, 

April 1, 2004.

95 Abuza, Militant Islam in Southeast Asia, 216.
55

political strategy may have been only marginally successful among Malays, it worked 

well with the country’s non-Malay voters.96 In the March 2004 general elections, 

Barisan Nasional candidates received 64 percent of the votes and won 90 percent of 

the seats in the Malaysian Parliament.97 Although PAS retained control of Kelantan 

state, UMNO also regained control of Terengganu state, where it immediately began 

reversing Shari’a provisions (bans on traditional female dancing, unisex hair salons, 

separate male and female checkout lines in stores) that PAS had implemented — as it 

had previously in Kelantan in the early 1990s.98

Retirement of Mahathir Mohammed

By the time of the 2004 general elections, however, Mahathir Mohammed was 

gone, having stepped down from all his offi ces except his seat in Parliament in October 

2003. Succeeding him was his Deputy Prime Minister, Abdullah Ahmad Badawi, 

former foreign minister and education minister in successive Mahathir governments. 

Mahathir had designated him Deputy Prime Minister after the dismissal and arrest of 

his predecessor, Anwar Ibrahim, in 1998. In the run-up to the 2004 elections, there was 

considerable doubt that Bedawi, an apparently less forceful individual than Mahathir, 

could play the dominant role in Malaysian politics that had characterized Mahathir’s 

22 years as Prime Minister.

Badawi succeeded, however, in separating himself, at least temporarily, from 

Mahathir’s political shadow. Running on a platform that promised to address problems 

of alleged corruption, cronyism, government ineffi ciency, and continuing rural 

poverty, Badawi surprised potential voters by arresting two key industrial leaders on 

charges of corruption prior to the election, and by reversing a Mahathir decision on 

the award of a major contract to build a railroad line that was widely believed to have 

been originally awarded for political rather than economic considerations.99 These 

measures that demonstrated an intent to govern in a way that responded to some of 

the dissatisfactions with the Mahathir regime no doubt contributed to his landslide 

election victory in April 2004. Badawi’s release of Anwar Ibrahim from prison later 

in the year (September 2) may also have been aimed at strengthening his popular 

base. Whether Badawi could survive the long knives of inter-party politics within the 

UMNO remained to be seen.

In selecting Badawi as his political successor, Mahathir appeared to have done well. 

From the standpoint of the Islamic factor in Malaysian politics, just as his co-optation 

96 Talk given by Heng Pek Koon (American University) at the U.S. Department of State, 

April 1, 2004.

97 Talk given by Osman Bakar (Georgetown University) at the U.S. Department of State, 

April 1, 2004.

98 Ioannis Gatsiounis, “Malaysia: Tug-of-War over Terengganu,” Asia Times Online, May 7, 2004. URL: 

http://www.atimes.com/atimes/Southeast_Asia/FG07Ae01.html. 99 Ioannis Gatsionnu, “Malaysia: Abdullah boleh-or Can He?” Asia Times Online, March 2, 2004. URL: 

http://www.atimes.com/atimes/Southeast_Asia/FC02Ae05.html. Accessed December 29, 2004.
56

Kampung King Mosque in Melaka, 

across Strait of Malacca from 

Sumatra, Indonesia, March 2004.

Source: NGA Research Center —

Ground Photography Collection.

of Anwar Ibrahim in 1982 had served him well politically, so his choice of Badawi in 

1998 had the appearance of being a political master stroke. Unlike Ibrahim, who had 

been an Islamic enthusiast, Badawi was formally educated in Islamic studies. Running 

on a slogan called Islam Hadhari (Civilized Islam) that called upon Malaysians to 

embrace modernity and the information age and to attend government schools rather 

than the traditional pondoks, generally run by the traditional (usually PAS-supporting)

`ulama, he would be a hard man to debate on Islamic grounds.

OUTLOOK

With the election of 2004, the UMNO and the Barisan Nasional continued to 

maintain the strong grasp on Malaysian politics it had held since the country gained 

independence in 1957. Challenged by a revival of Islamic sentiment since the 1970s, 

the party responded by co-opting Islamic values into its mechanism of governance. 

However, it had sought to embrace a vision of Islam that coexists with rapid economic 

development and prosperity. As a result, those with a more “fundamentalist” orientation 

have continued to be marginalized politically. This pattern is likely to endure for the 

foreseeable future. The Chinese and Indian elements of the electorate almost guarantee 

it, as does the ever growing urban, middle class Malay sector. As the 1995 landslide 

election of UMNO helped to give birth to the militant KMM movement, the frustrated 

reaction of the same PAS-related elements may give birth to a renewed militant element 

following the 2004 election. The regime is more alert to the threat to political stability 

posed by such a development in the post-9/11 world. Malaysian politics is likely to 

continue to be a rocky road, but continuity is likely to prevail over discontinuity — as 

it has in the past — for the foreseeable future

58

Map of Thailand.

Source: CIA.
59

CHAPTER 3

ISLAM IN THAILAND

For the Malay Muslims of southern Thailand the question has always been how 

to participate in the political process of a state based on a Buddhist cosmology... The 

process of national integration is synonymous with “cultural disintegration” from the 

perspective of many Malay Muslims.

 —Surin Pitsuwan

THE SULTANATE OF PATANI

The Malay Sultanate of Patani, situated in today’s southern Thailand, was established 

in the mid-15th century, soon after the foundation of the Sultanate of Malacca. The date 

usually given for the conversion to Islam of the previously existing raja of Langkasuka 

is 1457.100 The sultanate was situated on the east coast of the Malay peninsula and 

coincided with the present-day Thai provinces of Pattani,101 Yala, and Narathiwat.102

Like the other Muslim sultanates established in southeast Asia during this era, Patani 

was a trading state that facilitated east-west trade between China and other locations 

in the Far East with ports to the west. Its capital city, Patani, was located at the mouth 

of a river that drained into an extensive rice plain, and was strategically positioned to 

serve as the eastern terminus of an overland trading route across the peninsula.103 Its 

relative remote location on the northeast coast of the Malay peninsula isolated it from 

the advance of the Portuguese, Spanish, Dutch, and fi nally British trading settlements 

that began to be established in the region during the 16th century. 

The Decline of Patani

Although Patani fl ourished in the century after the Portuguese capture of Malacca 

in 1511, it began to decline economically in the early 17th century, about the time the 

Dutch established their permanent settlement at Batavia (Jakarta). Despite its economic 

decline, it emerged during the same century, along with Aceh in northwestern Sumatra, 

100 W.K. Che Man. Muslim Separatism: The Moros of Southern Philippines and the Malays of Southern 

Thailand (New York: Oxford University Press, 1990), 34.

101 The modern Thai province and city is spelled Pattani. The conventional Malay spelling of the 

traditional sultanate and its capital city is Patani. This difference in usage is followed in this study.

102 The fourth southern Thai province that is mostly Malay Muslim, Satun, was originally a part of the 

sultanate of Kedah (Malaysia), whose ruler formally ceded that portion of his sultanate to the Siamese king 

in 1843. 

103 Encyclopedia of Asian History. Ed. by Ainslie T. Embree (New York: Charles Scribner’s Sons, 1988), 

220.
60

as a principal center of Islamic scholarship and learning in southeast Asia, developing 

the reputation of being the “Cradle of Islam” on the Malay peninsula.104

An interesting aspect of Patani’s history during this period (1584 to mid-1600s) 

was rule by four successive queens (sultanah).105 The eventual threat to Patani’s 

independence came, not from advancing European power in the region, but from 

the expanding and consolidating Buddhist Siamese (Thai) Kingdom of Ayutthaya to 

the north.106 Although the sultan of Patani succeeded in defending himself from a 

number of attacks in the mid-18th century, he fi nally succumbed to Siamese power 

in 1785 — the same year the Sultan of Kedah leased the island of Penang to the 

English East India Company and was forced to pay annual tribute to the King of 

Ayutthaya, along with his fellow rulers to the south (the sultans of Kedah, Perlis, 

Kelantan, and Terengganu).

PATANI UNDER THAI RULE

The expansionist Chakkri dynasty, that continues to preside over Thailand today 

and was building its new capital at Bangkok during this period, likely would have 

sought the submission of the whole Malay peninsula had it not encountered the English 

104 First Encyclopaedia of Islam, 1913 – 1936, Vol VI, eds. M. Th. Houtsma, A.J. Wensinck, E. LeviProvencal, H.A.R. Gibb, and W. Heffening (New York: E.J. Brill, 1993), 1035. Also, Peter Chalk, “Militant 

Islamic Separatism in Southern Thailand,” in Jason F. Isaacson and Colin Rubenstein, eds., Islam in Asia: 

Changing Political Realities (New Brunswick, NJ: Transaction Publishers, 2002), 165.

105 Known as (1) Ratu Hijau (the Green Queen), (2) Ratu Biru (the Blue Queen), (3) Ratu Ungu (the 

Violet Queen), and (4) Ratu Kuning (the Yellow Queen), the period of their rule constitutes the “golden age” 

of Patani history, when the sultanate expanded its borders to include Kelantan and Terengganu, making it 

the most powerful Malay state after Johor in the south. Aside from a famed literary tradition that developed 

in this era and continues to this day [Virginia Matheson Hooker, “Patani,” in New Encyclopedia of Islam, 

ed. by C.E. Bosworth, E. van Donzel, W.P. Heinrichs, and G. LeComte, Vol. 8 (Leiden: E.J. Brill, 1995) 

285 – 286], Patani was famous for gun casting, of which two famous cannon measuring over six meters in 

length today grace the entrance of the Thai Ministry of Defense in Bangkok. See “The End of Langkasuka: 

The Rise and Fall of the Malay Kingdom of Patani,” Sejarah Melayu: A History of the Malay Peninsula. 

URL: http://www.sabrizain.demon.co.uk/malaya/kedah3.htm. Accessed January 3, 2005. 

106 Siam offi cially took the name Thailand (land of the free) only in 1939. Although the Tai (Thai) people 

who migrated from southern China gradually conquered the land of Siam in the 13th century, exerting 

their hegemony on other peoples previously inhabiting the land, it was not until the 20th century that 

considerations of nationalism — i.e., that Siam was the land of the Thai people-led to a formal decision to 

change the name of the country. Barbara Leitch LePoer, ed. Thailand: A Country Study (Washington, DC: 

HQ U.S. Army, 1987), 28. For contemporary writers looking backward, use of the term “Siam/Siamese” 

often seems archaic. Therefore, the term “Thai” is sometimes used in the text of this work, when (as a more 

modern coinage) use of the term “Siamese” actually would be more correct. Hopefully an esthetic balance 

has been achieved. 
61

presence on the peninsula.107 The British presence was in fact welcomed by the Thai 

king as a useful ally against arch-enemy Burma. As a result, a balance of power 

emerged that resulted over the long term in the emergence of independent Malaysia. 

The sultanate of Patani was not to be a part of this process, however. After a number 

of rebellions against Thai rule during the years 1791 – 1808, the Thai king partitioned 

Patani into seven smaller states,108 each with its own new sultan or raja appointed 

by the king but administered by the nearby Buddhist raja of Ligor (Songkhla). 

Although this measure of divide and rule made it easier to assure Thai domination of 

the region, it did not prevent yet another uprising in 1832, and again in 1838, that the 

Thai government suppressed with particular brutality, devastating the countryside and 

transforming the once prosperous sultanate into the economically backward region it 

has since remained.

Following the revolt of 1838, the region of Pattani remained relatively quiescent 

under Thai rule, perhaps in part because the central government left it alone and 

engaged in minimum interference in local affairs. This changed during the latter years 

of modernizing Thai monarch, Chulalongkorn (Rama V, 1868 – 1910), who, among 

other things, placed an emphasis on modern communications, including the railroad 

that was completed as far as the Malay border soon after his death. He also began the 

development of a modern education system. Although the new system of government 

schools did not reach Pattani during his reign, it would eventually pose a challenge to 

the traditional `ulama-run pondok schools whereby Islamic tradition was transmitted. 

Most importantly for Pattani was the king’s effort, beginning in 1893, to implement 

a more modern system of government administration. In 1902, the seven states into 

which the old sultanate of Patani had been divided in 1808 were reconsolidated into a 

single province under the direction of a Siamese High Commissioner. Although each 

former state retained its Malay ruler, each ruler was advised by a Siamese offi cer 

who reported directly to the Siamese High Commissioner in Pattani. This system, 

which closely resembled the “residency” system established by the Dutch in Java in 

the 1830s and the British in some of the Malay states beginning in 1874, had as its aim 

the elimination of traditional indirect forms of rule and the consolidation of central 

authority as a basis for more uniform rule throughout the kingdom. All offi cials, 

including the local rulers, moreover, were salaried and forbidden to collect fees for 

107 The Thai view is that once the authority of Siam had extended over the whole of the Malay peninsula, 

whose local rulers held their title from the King of Siam. The conversion or changeover of many of these 

rulers and peoples to Islam was part of an expression of rebellion or independence from Thai suzerainty. 

Behind this conversion to Islam were the expansionist policies of the sultan of Malacca who was challenging 

Thai hegemony on the peninsula. Beset by many other challenges, the kings of Siam were never able to 

reassert their hegemony over parts of the peninsula until the emergence of the Chakkri dynasty in 1767. 

See Sir John Malcolm, “Malcolm (4 Kings),” LoveToKnow 1911 Online Encyclopedia. (c)2003,2004 

LoveToKnow, URL: http://65.191encyclopedia.org/M/MA/MALCOLM_4_KINGS_.htm. Accessed January 

3, 2005.

108 Pattani, Nhongchik, Reman, Rangae, Saiburi, Yala and Yaring. “Briefi ng: A brief introduction to the 

Malay Kingdom of Patani,” from Islamic Human Rights Commission Online. URL: http://www.ihrc.org. 

uk/show.php?id-1342. Accessed January 3, 2005. 
62

services rendered or to exact forced labor. In this manner, as in the neighboring Malay 

states and in the Dutch East Indies, the traditional Muslim ruling class was transformed 

into a salaried sector of the Siamese central government.109

Consolidation of Thai Rule

The new administration was not implemented in Pattani without resistance, however, 

and in 1906 the province was redivided into four provinces as a means of combating 

the unifi ed resistance demonstrated by the native Malays to the changes being imposed 

on their region. Later, the division of old Patani was reduced to the three provinces that 

continue to exist today.

Control of provincial administration was of growing importance to the Thai 

government, largely because of increasing pressure being exerted on Siam by France 

and Britain. The French occupation of Cochin China in 1863 had forced Siam to 

formally relinquish its claim to Cambodia in 1867 — except for the provinces of 

Siem Reap and Battambang. Then in 1885, Britain completed its conquest of Burma, 

annexing portions of northern Burma claimed by the Thai monarchy. Meanwhile, as 

France consolidated its control of all of Vietnam in the 1880s, it began to assert claims 

on Thai-controlled Laos, which Siam was forcibly forced to cede to French control in 

1893. Then in 1907, France forced Thailand to cede Battambang and Siem Reap to 

Cambodia. 

Under pressure from Britain to defi ne the border between Siam and the Malay 

states over which it had increasing infl uence, King Chulalongkorn did so in 1909 

by abandoning his claims to Perlis, Kedah, Kelantan, and Terenggannu in return 

for a major loan to complete his railroad to the Malayan frontier. Pattani, always a 

troublesome region with very few Thais or Buddhists among its residents, remained 

a part of Siam. The conclusion of the Anglo-Siamese Treaty of 1909 that delineated 

this border brought an end to European imperial expansion in southeast Asia, as both 

England and France began to view Siam as a convenient buffer, reducing friction 

between the two rivals that soon would be allies in World War I. At the same time, 

the fi nal borders of the Siamese state were drawn, receiving international recognition 

as such, and Siam was poised to evolve as a territorially-based, modern nation state, 

rather than as an empire of the Thai kings whose borders historically had ebbed and 

fl owed depending on the strength of the monarchy.

Continued Pattani Resistance

The period between 1909 and the Siamese revolution of 1932 witnessed a number 

of uprisings against Thai rule in the Pattani region. Close intermarital links between 

109 Clive Christie, A Modern History of Southeast Asia (New York: I.B. Tauris, 2000), 175.
63

the Patani and Kelantan royal families led Siamese authorities to suspect “outside” 

intervention and support from Kelantan, and accordingly to strengthen policies of 

centralization, especially in the areas of taxation, education, and in requiring use 

of the Thai languages, both in schools and government offi ces. Such policies only 

strengthened opposition to Thai rule and helped to provoke violent outbreaks, such as 

the Patani revolt of February-March 1923.110

UNDER THE THAI REVOLUTIONARY REGIME

The Siamese revolution that occurred by a bloodless coup d’état in June 1932 

brought to power in Bangkok a group of younger, “nationalist” military and civilian 

leaders whose action was directed, not against the king who remains the symbol of the 

Thai nation until today, but against his coterie of conservative royal ministers, whom 

the revolutionaries felt were holding the country back from emerging as a modern 

nation state. Their goal, which they moved quickly and successfully to implement, was 

to transform the traditional absolute monarchy into a limited constitutional monarchy, 

governed increasingly by representative institutions such as the unicameral National 

Assembly that the “promoters” rapidly brought into being within a year. 

Although the unity of the new nationalist leadership soon broke down over various 

issues and has never provided the country with a truly “stable” government, the leaders 

remained unifi ed on the “nationalist” character of their revolution, an attitude that led 

to a change in the name of the state to “Thailand” in 1939, and a view that all citizens 

of the Thai state (no longer simply subjects of the Thai king) were Thai nationals who 

should participate fully in the institutions and culture of the Thai people. 

Although the policies of the new nationalist leaders of Thailand were almost wholly 

secular in nature, Thai culture is overwhelmingly Theravada Buddhist in orientation, 

a circumstance that led the Malay Muslims of Pattani to feel even more marginalized 

in the larger society whose new leadership clearly wanted them to be a part. The 

replacement of civilian leadership by a more authoritarian military leadership in 1938 

accelerated this nationalization process even further.111

World War II

During World War II, as the Japanese invaded southeast Asia in late 1941, taking 

over French Indochina, the Philippines, the Malay peninsula, and the Dutch East Indies 

110 Christie, A Modern History of Southeast Asia: Decolonization, Nationalism and Separatism (London: 

Tauris Academic Studies, 1996), 175 – 176. 

111 LePoer, Barbara Leitch, ed. Thailand: A Country Study. Department of the Army Pamphlet 550 – 53 

(Washington, DC: Federal Research Division, Library of Congress, 1987), 26 – 28. Also Christie, Modern 

History of Southeast Asia, 176 – 177.
64

in early 1942, the ultranationalist Thai military regime of Phibun (later Field Marshal 

Luang Plaek Phibunsongkhram), probably as much because of ideological affi nity as 

well as reasons of Realpolitik, allied itself with Japan and permitted Japanese forces 

to enter the Malay peninsula from the north in 1941 at the coast near Pattani.112 As a 

reward for its cooperation, Thailand received from the Japanese during the war parts of 

its former territories in Laos, Cambodia, and Burma as well as the four Malay states of 

Kelantan, Terengganu, Kedah, and Perlis. The Thai alliance with Japan and its January 

1942 declaration of war against Britain and the United States,113 not to mention the 

recovery of the Malay states, made Britain and Thailand antagonists during the war. 

As a result, whereas most Malays during the war collaborated with the Japanese with 

the nationalistic aim of eventually securing their independence from the British or the 

Dutch, many Pattani Malays collaborated with the British against the Thai regime.

The leader of this movement was Tenku Mahmud Mahyiddeen, the second son 

of the last sultan (or raja) of Patani, Tenku Abdul Kadir, who had been sent into 

exile by the Thai government earlier in the century. A member of the Kelantan civil 

service from 1933, Tenku Mahmud escaped with the British army to India following 

the Japanese invasion. “There he played a leading role recruiting Malay volunteers for 

Force 136, the organization that was coordinating guerrilla activity in Malaya against 

the Japanese.”114 The bulk of this activity took place in the Pattani region of southern 

Thailand, where anti-Thai sentiment was strong, and where the British were planning 

for a counter-invasion of the Malay peninsula. 

Last Gasp Toward Patani Secession

Tenku Mahmud hoped that British success in the war would lead to a liberation of 

Patani from Thai rule. Indeed in November 1945, shortly after the end of the war, seven 

leading members of the traditional Malay ruling elite of Patani addressed a formal 

petition to London requesting “that the British Government may have the kindness to 

release our country and ourselves from the pressure of Siam, because we do not wish 

to remain any longer under the Siamese Government.”115

112 Christie, Modern History of Southeast Asia, 178.

113 An interesting and signifi cant sidelight of the Thai declaration of war against the United States was 

that it was never formally presented in Washington by the Thai ambassador — Seni Pramoj, later Prime 

Minister of Thailand after the war — who instead organized and led a “Free Thai Movement’’ that cooperated 

with the United States Offi ce of Strategic Services (OSS) during the war. Accordingly, the United States 

never declared war on Thailand and at the end of the war did not consider it a belligerent. Thailand: A 

Country Study, 30.

114 Christie, Modern History of Southeast Asia, 178.

115 Full text in Christie, Modern History of Southeast Asia, 227 – 230. Notably, the text asks neither for 

Pattani independence or affi liation with the Malay Federation. It consists mainly of a detailing of Patani 

grievances with Thai rule and a request for liberation from Thai rule.
65

The moment was probably the most opportune time the Malay Muslims of Patani 

have had before or since to realize their general desire for secession from Thailand. 

It is clear that the British government seriously considered the proposal, and some 

members of the government favored a positive response as a means of “punishing” 

Thailand for its stance in the war. In the end, however, it made no response to the 

proposal. The reasons for this were perhaps several.

A 1944 change of government in Thailand had brought to power new leaders who 

gradually were able to repudiate the former regime’s agreements with Japan and 

covertly give free access to allied agents operating in Thailand. Thus Thailand had 

effectively changed sides during the war, and could claim it no longer was the hostile 

power it had been at the start of the war. 

Moreover, British support for the Malay Union in British Malaya as a means of 

“punishing” the Malays for their general support of the Japanese during the war 

probably worked to the detriment of the Patani Malays, whose cause was not unrelated 

to the cause of their fellow Malays lower on the peninsula. The powerful Malay 

nationalist response that led Britain to reverse its position on the Malay Union in favor 

of a Malay Federation in February 1948 was echoed in the Patani region as well. But 

here it was expressed as bitterness, for it was too late. In January 1946, Britain and 

Thailand had signed a post-war treaty in which the latter agreeably returned Kelantan, 

Terengganu, Kedah, and Perlis, as well as portions of Burma it had taken over during 

the war, to the British in return for no further territorial concessions.116

Finally, a key indirect role probably had been played by the United States, which in 

the latter stages of World War II began to view Thailand as a key linchpin of its strategic 

interests in southeast Asia. The U.S. communicated to Britain that it was not “prepared 

to accept any post-war arrangement that would impair Thai sovereignty.”117

New “Islam-Friendly” Policies Toward Pattani

The new Thai government that had covertly switched sides in the war with Japan 

was also prepared to deal differently and more constructively with its southern MalayMuslim population than its predecessor regime had been. Perhaps infl uenced by the 

threat that Britain might lay claim to the Pattani region for the Malay Federation, it 

enacted in late 1945 a “Patronage of Islam Act,” which sought to integrate Islam into 

the structure of state governance. 

Among other things, the Act established a formal Islamic hierarchical structure 

comprised of state-appointed `ulama headed by a chularajmontri (chief cleric) 

appointed by the King himself. Also established by the Act was a National Council for 

116 Christie, Modern History of Southeast Asia, 181.

117 Christie, Modern History of Southeast Asia, 181.
66

Islamic Affairs and Provincial Councils for Islamic Affairs “in every province where 

there are a substantial number of Thai Muslims.” Very quickly, in 1946 and 1947, the 

government allowed itself to be infl uenced by these new institutions to restore certain 

prohibitions that had been imposed by the pro-Japanese regime-Friday as a religious 

holiday in Muslim areas and the applicability of Islamic law for Muslims in the areas 

of marriage, family, and inheritance. In addition, the government worked closely with 

the new Islamic institutions to develop regulations for the registering of mosques, 

election of mosque councils, and the appointment of mosque offi cials.118

Although the civilian leadership responsible for these reforms was overthrown by 

coup d’état in November 1947 by the same military clique it had replaced in 1944, 

an event that energized Pattani leaders to make renewed efforts to gain international 

recognition for separation from Thailand, the new regime did not reverse these reforms 

that continue to form the basis of the relationship between the Thai state and Islam 

until today. 

The Continuing Language Issue

One area the more liberal civilian leaders had not touched, however, and the new 

military junta assiduously avoided, was the language issue-that Thai rather than Malay 

should be the language of instruction in Thai schools. The language issue, rather than 

Islam itself, increasingly became the point of contention between Pattani separatists 

and state authorities until the last years of the 20th century. The reforms, by integrating 

Islamic law, or at least portions of it, into the structure of state authority for Muslims, 

in fact transformed Thailand into a relatively “Islam-friendly” state into which “Thai” 

Muslims possessed equal opportunity and even perhaps some advantages with regard 

to access to higher education and social mobility, but “Malay Muslims” continued to 

experience prejudice and unequal treatment with respect to the larger society.

The Growth of Islam in Thailand

The “Islam-friendly” reforms of the late 1940s had the long-term effect of actually 

facilitating Muslim immigration into Thailand, mainly from India (including Pakistan/

Bangladesh) and China. Hence, today an estimated 300,000 of the country’s 2.5 million 

Muslims who reside primarily in northern Thailand and in the region of Bangkok 

practice Islam freely but otherwise are gradually assimilated into Thai culture through 

education and intermarriage.119

118 Christie, Modern History of Southeast Asia, 182.

119 Preeda Prapertchob, “Islam and Civil Society in Thailand: The Role of NGOs,” in Islam and Civil 

Society in Southeast Asia, ed. by Nakamura Mitsuo, Sharon Siddique, and Omar Farouk Bajunid (Singapore: 

Institute of Southeast Asian Studies, 2001), 111 – 112.
67

A high degree of assimilation has also been achieved in the southwestern Malay 

province of Satun, across the Malaysian border from Kedah, where an absence of lines 

of communication forms an effective barrier between the province and its southern 

Malaysian neighbor.120

In the southeastern Malay provinces of Pattani, Yala, and Narathiwat, it has been 

a different story. Although there are many examples of individuals and families who 

have successfully assimilated into Thai society,121 a critical mass remains that resists 

assimilation, attempts to demonstrate ignorance of the Thai language, and keeps alive 

the dream of separation from Thailand.

Diminished Signifi cance of Pattani Issue During Cold War

The eruption in 1948 of the Communist insurgency in Malaya and the emergence 

of the Thai-Malay border area as a haven of refuge for the mainly Chinese communist 

insurgents placed a premium on close British-Thai relations in order to secure the 

Thai-Malay border. The issue of Pattani separatism was accordingly overshadowed by 

issues that from the larger international perspective seemed far more signifi cant, and 

Pattani separatist hopes that had seemed so near to fruition only three years before now 

appeared to be dashed forever.

Despite continued Thai efforts to achieve assimilation of the old Patani region, it 

has until now “remained a ‘zone of dissidence,’ with intermittent outbreaks of guerrilla 

activity and, at best, only a sullen submission to Thai rule.”122 A key to maintaining 

the traditional Muslim-Malay culture of this region was the continued fl ourishing of 

the long-established pondok system of private Islamic boarding schools.123 Despite 

the earlier establishment of government schools that provided a mandatory sevenyear curriculum in the Thai language, including Buddhist as well as Islamic religious 

instruction, the pondok system continued to fl ourish.124

120 Christie, Modern History of Southeast Asia, 187.

121 Notable examples are Dr. Surin Pitsuwan, who served as Thai Foreign Minister in the late 1990s, 

and Wan Muhammad Noor Matha, former President (Speaker) of the Thai National Assembly. Prapertchob, 

“Islam and Civil Society in Thailand,” 104 – 105.

122 Christie, Modern History of Southeast Asia, 187.

123 See Hasan Madmarn, The Pondok and the Madrasah in Patani (Bangi: Universiti Kebangsaan 

Malaysia Press, 1999). 

124 Parents typically sent their children for the fi rst seven years to the government-operated elementary 

school, then on to the pondok for intermediate and higher education, if they could afford it and wished such 

a destiny for their (usually male) child. See Department of the Army, Ethnographic Study Series: Minority 

Groups in Thailand, Chapter 16, “The Malays’’ (Washington, DC: HQ, Department of the Army, February 

1970), 1029 – 1030. This 54-page chapter is a fi ne ethnographic survey of the Malay Muslims of southern 

Thailand and is highly recommended as a detailed overview of Malay social life in Thailand. See also 

Madmarn, The Pondok and the Madrasah in Patani, 74.
68

THE PATTANI INSURGENCY

Beginning in 1960 the Thai government undertook steps to bring the pondok schools 

under state supervision as well. A key aspect of the program was a requirement that all 

pondoks be registered with the Ministry of Education and add to their curricula certain 

secular subjects required of all Thai schools. Although Malay was not eliminated as a 

language of instruction, registration required Thai to be added as a second language of 

instruction. Registered schools were eligible to receive state funding and were subject 

to state inspections, but could remain “private” schools. They were also obliged to 

provide educational authorities with lists of teachers and pupils. Unregistered schools 

were considered to be operating “illegally” and subject to closure. As a result, some 

150 of an estimated 355 schools then operating closed in protest, but by 1971 some 

400 pondoks were registered as “legal” private schools. In 2004, it was alleged 

that 127 unregistered pondoks were still operating in the Malay region of southern 

Thailand.125

If the pondok system remained the primary means used by southern Malays to 

preserve and transmit Islamic teachings and Malay culture, the clear effort by Thai 

authorities in the early 1960s to gradually compromise the independent character of 

these schools led some political activists to devise new means to pursue the cause of 

Malay separatism. It was just at this time and in apparent reaction to this effort that 

a variety of new political organizations, some with a militant agenda, sprang up to 

pursue the struggle to preserve Malay heritage in other ways. 

The Barisan Revolusi Nasional

One of the fi rst was the National Revolutionary Front (Barisan Revolusi Nasional—

BRN), established by a group of former pondok teachers and led by Ustaz Haji Abdul 

Karim, himself the owner of a pondok in Narathiwat province, who, rather than 

submit to Thai authority, took to the jungle to organize a revolutionary opposition.126

Identifi ed in 2004 as the “largest and best organized of the three main insurgent factions 

operating in southern Thailand,127 the BRN from the beginning was fully committed 

to armed struggle, totally denying the legitimacy of Thai rule over Muslim Malays, 

and committed to the reconstruction of a Muslim-Malay state of Pattani in southern 

Thailand. The emergence of the BRN coincided with the end of “the Emergency” in 

neighboring Malaya. It may have refl ected a change of strategy in the Communist 

Party of Malaya (CPM), with which the BRN became closely allied, to focus on Pattani 

national liberation as a prologue to the establishment of a unifi ed, socialist Malay

125 Madmarn, The Pondok and the Madrasah in Patani, 74. Also Anthony Davis, “Thailand Confronts 

Separatist Violence in its Muslim South,” Jane’s Intelligence Review, March 2004, 21 – 22.

126 Anthony Davis, “Southern Thai Insurgency Gains Fresh Momentum,” Jane’s Intelligence Review, 

August 2004, 19.

127 Davis, “Southern Thai Insurgency Gains Fresh Momentum,” 19.
69

nation “stretching from Pattani to Singapore, governed by one head of state and united 

under one common fl ag.” Such was the identical view of both parties.128

Its alliance with the CPM, its socialist program, and its emphasis on Malay 

nationalism tended to identify the BRN as a secular rather than Islamist party, although 

its manifestos continued to be cast in religious terminology-Islamic socialism being the 

promotion of a just and prosperous society sanctioned by God and Malay nationalism 

being an expression of God’s oneness and unity. The BRN was in many respects a 

“national” or “people’s” liberation movement typical of many such movements 

throughout the “Third World” in the 1960s and 1970s that benefi ted in varying degrees 

from Soviet or communist-bloc support. Like other groups with whom it competed in 

striving for the liberation of Pattani from Thai rule, it engaged in a variety of violent 

actions-ambushes, assassinations, kidnappings, extortion, sabotage, and bomb attacksgenerally designed to promote an atmosphere of lawlessness in the region, a sense of 

insecurity for ethnic Thais living there, and an intolerable burden for Thai offi cials 

trying to govern the area. The main targets were those symbols of Thai authority that 

were “considered to pose the greatest threat to Malay-Muslim culture and identity,” 

in particular schools, teachers, local government offi cials and administrators, and 

Buddhist settlers in the south.129

PULO

Although the BRN made its mark in the 1960s and 1970s as a viable insurgent 

organization, its strong left-wing agenda did not enable it to achieve mass appeal 

among the essentially conservative Malay-Muslim population of southern Thailand, 

and it was eventually overshadowed by a competing insurgent group, the Pattani United 

Liberation Organization (PULO). Organized “in 1968 by Kabir Abdul Rahman, an 

Islamic scholar who had become disillusioned with what he saw as the ‘limited’ and 

‘ineffectual’ nature of the established Malay opposition in Pattani,” PULO “grouped 

together a younger, more militant generation of Thai Muslims — many of whom had 

been radicalized while studying overseas — becoming an active insurgency with the 

politicization of Malay students in the early 1970s.”130

The growth of PULO coincided with the effl orescence of Islamic revivalism in 

neighboring Malaysia during the 1970s and refl ected a similar trend that soon followed 

128 Peter Chalk, “Militant Islamic Separatism in Southern Thailand,” in Jason F. Isaacson and Colin 

Rubenstein, eds., Islam in Asia: Changing Political Realities (New Brunswick, NJ: Transaction Publishers, 

2002), 169 – 170.

129 Chalk, “Militant Islamic Separatism in Southern Thailand,” 168 – 169.

130 Chalk, “Militant Islamic Separatism in Southern Thailand,” 171.
70

in the Malay regions of southern Thailand during this same period.131 Eschewing 

the left-wing rhetoric of the BRN, PULO positioned itself as a more strictly MalayMuslim nationalist organization that sought and received its external support from 

sources in the Muslim world. Libya and Syria were two countries that provided degrees 

of support, and some PULO fi ghters received training from the Palestine Liberation 

Organization (PLO) in Lebanon.132

More importantly, PULO received strong popular support from Malays in Malaysia 

and more specifi cally from the Islamic opposition party in Malaysia, the Parti Islam 

seMalaysia (PAS) that controlled neighboring Kelantan state and for which support 

for Muslim separatism in Thailand served as a useful rallying cry. Although the ruling 

United Malay National Organization (UMNO) that governed Malaysia found it in the 

national interest to collaborate closely with neighboring Thailand over the security of 

their joint border, the issue remained a delicate one that the Malaysian government 

could not push too vigorously without augmenting popular support for its PAS rival. 

Accordingly, despite close joint Thai-Malaysian cooperation over border security, 

Kelantan especially remained a safe haven for PULO activists and a transit point for 

fund transfers and fi ghters moving in and out of Thailand. Ostensibly an organization 

that “placed priority on improving the standard of education among the southern 

Malay population as well as fostering and nurturing their political consciousness and 

national sentiments,” PULO, possibly in part to keep pace with the BRN and other 

rival organizations, sanctioned violence as part of its secessionist struggle. PULO 

violence was carried out by its military arm, the Pattani United Liberation Army 

(PULA), which claimed responsibility for a number of bombing and arson attacks 

on the same types of targets — symbols of Thai rule-in southern Thailand, as well as 

occasionally in Bangkok.133

Other Resistance Groups

Although the BRN and PULO were the principal resistance movements against 

continuing Thai rule in southern Thailand during the 1960s – 1980s, a weakness of 

the resistance movement in general was the plethora of other movements that also 

emerged, either as break-away movements or as new initiatives in other sectors of 

Malay-Muslim Thailand. Among these were the Barisan Nasional Pembebasan 

131 Prapertchob, “Islam and Civil Society in Thailand,” 109, notes that the 1979 Islamic revolution in 

Iran and the global Islamic resurgence that that revolution represented was the key watershed event for the 

revival of Islamic sentiments in southern Thailand, symbolized by the widespread appearance of female 

hijab, a type of attire that in the past had not been widespread, but “limited only to the time of prayer or 

for the old people in the rural areas or for people who had performed the hajj and during particular Muslim 

festivities and ceremonies.”

132 Zachary Abuza, Militant Islam in Southeast Asia: Crucible of Terror (Boulder, CO: Lynn Reinner 

Publishers, 2003), 79.

133 Chalk, “Militant Islamic Separatism in Southern Thailand,” 172.
71

(BNPP), formed in 1971; the Sabil-illah, established in 1975 – 1976; and Black 

December 1902, a shadowy organization that simply refl ected the date when the old 

Pattani sultanate was formally incorporated into the Thai kingdom.134

The Other Side of the Coin

Adding to the complexity of the situation, yet another wholly different organization 

dating from the early 1960s was the Thai Muslim Student Association (TMSA), 

“established to promote and preserve the collective interests of the ummah in Thailand 

in general and the educated Muslim youths in particular.” Somewhat analogous to the 

Malaysian Islamic Youth Movement (ABIM), established in neighboring Malaysia a 

decade later, the TMSA sought to avoid confl ict with the government, and instead to 

win the respect of Thai authorities for Malay culture as part of the diverse nature of 

Thai society. 

Placing an emphasis on leadership training through seminars, workshops and student 

work camps, especially in rural areas, the TMSA sought to respond to liberal trends in 

Thai society that were prepared to accept Islam as a component of Thai culture and to 

permit the Malay Muslims the maximum degree of self-government. Many products 

of this organization did indeed emerge as successful politicians, university professors, 

executives, senior government offi cials, and businessmen, including the former Thai 

foreign minister, Dr. Surin Pitsuwan, and President of the Thai National Assembly, 

Wan Muhammad Noor Matha. As an organization of student activists, the TMSA was 

also deeply involved in the pan-Thai student revolution of the early 1970s that fi nally 

toppled the military dictatorship of Thanom Kittikachorn in 1973.135

Thai Countermeasures

Despite the persistence of Malay-Muslim insurgent activity in southern Thailand 

from the 1960s through the 1980s, Thai government authority, focused on its 

Fourth Army Region Southern Border Provinces Administration Center (SBPAC) 

headquartered in Pattani, managed to prevent the resistance from becoming the largescale popular movement PULO in particular sought to make it. Although Thai forces 

were often brutal toward villages thought to be harboring insurgents, Thai policy in 

general remained assimilation, permitting Muslims to practice their religion freely. This 

included adjudicating legal cases between Muslims in Islamic courts in accordance 

with Islamic law, fostering Muslim upward mobility within Thai society for those who 

134 Chalk, “Militant Islamic Separatism in Southern Thailand,” 182 – 183.

135 Prapertchob, “Islam and Civil Society in Thailand,” 105 – 106.
72

adapted to Thai cultural norms, and generating projects designed to raise the economic 

standards of the Muslim inhabitants of southern Thailand.136

The combination of approaches led in the 1980s to a gradual overcoming of the 

insurgency so that by the end of the decade Muslim insurgents were assessed to number 

no more than 300 – 500, whereas at their peak in the mid-1970s they had numbered 

on the order of 3,000. The insurgency seemed over, and in 1993 the Thai government 

offered amnesty to those willing to lay down their arms. Nearly half accepted these 

terms, leaving the estimated remaining 150 – 200 Malay militants offi cially defi ned 

as outlaws, drug smugglers, gun-runners, bank robbers, terrorists — all of which they 

were — hiding out in the jungles of southern Thailand or northern Malaysia.137

136 Thai policy toward the insurgency fi nally came to be based on Prime Minister’s Orders 66/2523 

and 65/2525, issued by the government of Prime Minister Prem Tinsulanonda in the late 1970s. Directed 

primarily against the Thai Communist Party (TCP) threat, a far more signifi cant insurgent threat than that 

of the Malay-Muslim south, the same principles were applied in the south as elsewhere in the country, with 

considerable short-term success. Targeting sources of corruption and class differentiation in Thai society as 

well as the militant movements opposed to the government, the policy stressed economic development and 

maximum political participation at the local level. See Paragraph 6, “Thai Government Policies,” in Primer: 

Muslim Separatism in Southern Thailand. Prepared by the Virtual Information Center of HQ USCINCPAC. 

URL: http://www.vic-info.org/SEAsia/ThailandPage.htm. Accessed February 3, 2005.

137 Abuza, Militant Islam in Southeast Asia, 78.

Predominantly Muslim Sectors of Southern Thailand and 

Northern Malaysia.

Source: Author.
73

Although instances of insurgent violence-bombings of schools, drive-by shootings, 

and arson attacks — continued during the 1990s, these were far more sporadic, less part 

of a pattern or concerted strategy, and more easily construed solely as criminal acts. 

From the standpoint of the Thai government and most analysts observing Thai affairs, 

Thailand had effectively contained the Malay-Muslim separatist movement, as it had 

the communist insurgency in other parts of the country, with successful policies aimed 

at dealing harshly with the insurgents and seeking to eliminate the perceived causes 

and rationale for the insurgent activity.

FROM NATIONALISM TO ISLAM

With regard to southern Thailand, however, this judgment proved to be premature. 

In fact, Malay-Muslim separatist sentiment was passing through a quiet phase as 

it slowly transformed from one form into another — from what had been a largely 

nationalistic, ethnic Malay-based resistance to a cause that was more deeply rooted in 

Islamic religious sentiment. According to Prapertchob, this transformation began in 

the early 1980s, fully a decade after its appearance in neighboring Malaysia. 

Largely inspired, in Prapertchob’s view, by the success of the Iranian revolution, the 

movement manifested itself in several ways. The most obvious manifestation was the 

hijab movement, a widespread tendency for Muslim women who previously had had 

no such tradition in southern Thailand to adopt a head covering and long, full-bodied 

dress for all aspects of their public lives. A second was the widespread proliferation 

of the apolitical Jemaat Tabligh and Darul Arqam movements, apparently with Thai 

government support, that had fl ourished in neighboring Malaysia in the 1970s and 

now spread into Thailand in the 1980s.138 Increased mosque attendance, the building 

of a signifi cant number of new mosques, and construction of the Saudi-funded Yala 

Islamic College were yet other manifestations of this Islamic revival.

Less noticed during this quiet period of the late 1980s and early 1990s was the 

gradual disappearance of young men who might otherwise have been engaged in 

insurgent operations in southern Thailand. Although unnoted at the time, their absence 

became apparent as they began to return from Afghanistan and perhaps other fi ghting 

fronts in the early to mid-1990s. Again, as in neighboring Malaysia, in 1995 a group of 

these Afghan veterans coalesced into a new organization, GMIP (Gerakan Mujahideen 

Islam Pattani, or Pattani Islamic Mujahideen Movement), under the leadership of 

Afghan veteran Nasori “Sori” Saesaeng (aka Wae Ka Raeh).139

138 Prapertchob, “Islam and Civil Society in Thailand,” 109 – 111.

139 Davis, “Thailand Faces up to Southern Extremist Threat,” 13.
74

Formation of GMIP

The appearance of GMIP in southern Thailand almost simultaneously with the 

formation of a parallel organization, the KMM (Kampulan Mujahidin Malaysia), in 

neighboring Kelantan state cannot be explained as pure coincidence. The common 

experience of studying and training in Afghanistan and/or Pakistan and association, 

whether formal or informal, with Jemaah Islamiyah and al-Qa'ida suggests a 

commonality of purpose and commitment to mutual support, if not a more formal 

alliance or union as parts of a single larger organization.

As with the Malaysian KMM, the period 1995 – 2000 was a time of training, 

preparation, and planning for the GMIP. The year 1995 also brought a split in the old 

PULO and the formation of a more militant new PULO, also called the BNB (Barisan 

Nasional Baru), as well as yet another small radical group called the Tantra Jihad 

Islam (TIJ). Although historically loath to coordinate their operational activities, in 

mid-1997 the groups did come together to form Bersatu (Solidarity), a tactical alliance 

between the old, more nationalist groups in an effort to “refocus national and regional 

attention on the ‘southern question.’”140 Following their agreement, during the period 

August 1997 – January 1998 no fewer than 33 separate attacks were carried out against 

symbols of Thai rule in southern Thailand, resulting in nine deaths, several dozen 

injuries, and considerable economic damage in a campaign of violence the region had 

not seen since the early 1980s.141 Although the Thai government responded forcefully 

to contain this new outbreak of insurgent activity, its success in doing so by early 

1998 was in part due to new Malaysian cooperation in arresting insurgent leaders 

taking refuge in neighboring Kelantan state. Whereas Malaysian Prime Minister 

Mahathir Mohammed previously had adopted a general hands-off attitude toward 

Malay insurgent activity in Thailand, on this occasion he responded decisively to Thai 

appeals to guarantee the security of their common border.142

The Bersati-led outbreak of violence coincided with the 1997 Asian fi nancial 

crisis that had the impact of undermining the political leadership of both Thailand 

and Malaysia, and in this situation Malaysia’s Mahathir perceived cracking down on 

insurgent refugees from Thailand as a means of striking out against his own political 

rival, the Parti Islam seMalaysia (PAS).Centered on Kelantan state, PAS both gave 

safe haven to the rebels from Thailand and was gaining political strength at Mahathir’s 

expense due to the Asian fi nancial crisis.

The failure of the Bersati uprising undermined the continuing appeal of the 

traditional separatist parties, as many traditional activists began surrendering to Thai 

authorities or fl ed abroad into exile. As would soon become apparent, ongoing resistance 

to Thai authority in southern Thailand would increasingly express itself in Islamist 

140 Chalk, “Militant Islamic Separatism in Southern Thailand,” 175, 183.

141 Chalk, “Militant Islamic Separatism in Southern Thailand,” 175.

142 Chalk, “Militant Islamic Separatism in Southern Thailand,” 176.
75

rather than nationalist terms. This was not apparent at the moment, however, as Thai 

government authorities tended to be confi dent that Malay separatist sentiments had 

been compromised and that any continuing insurgent-like activities — drug-running 

as a money-making activity, illegal arms traffi cking, bank robberies, assassinations, 

bombings — were solely ongoing criminal activity characteristic of the economically 

backward southern region of the country.

REVIVAL OF THE INSURGENCY

Later reporting indicated that the late 1990s was a period of intensive training 

for new cadres of Islamist militants in southern Thailand that involved members of 

the KMM in Malaysia and others who “spoke Malay with an Indonesian accent.” 

Instruction was said to take place covertly at night in buildings in both urban and rural 

areas and included classes relating to the history of the Malay sultanate of Patani, the 

concept of jihad, and physical as well as weapons training. Maintaining the clandestine 

nature of the activities of the assembled cadres was said to have been of paramount 

concern. Most instructors and trainees wore ski masks to conceal individual identities, 

and the greatest stress was placed on the importance of security.143

Although Thai authorities until early 2005 remained in denial concerning the 

possibility of linkages between Thai separatists and the transnational Jemaah Islamiyah

(JI), it seems likely that this clandestine jihadist training activity in southern Thailand 

was JI-related, involving Thai Muslim, Malaysian, Indonesian, possibly Filipino, and 

perhaps jihadist Muslims of even other nationalities.

Although instances of bombings and other insurgent-type activities continued 

sporadically during this period, Thai authorities persisted in asserting that although 

terrorist groups continued to exist in the south they lacked the organization and 

fi nancial support to mount a viable insurgent threat, as they had in the 1960s into the 

1980s. Accordingly, during the summer of 2001, soon after the election of tycoon 

Thaksin Shinawatra as the new Prime Minister of Thailand, the government began the 

process of dismantling its Southern Border Provinces Administration Center (SBPAC) 

that had long been the focus of Thai anti-insurgency operations in the south.144

Thai Government Remains in Denial

Incredibly, this decision of the Thai government followed the fi rst operation carried 

out by the Jemaah Islamiyah in Thailand on April 7, 2001, the bombing of the Hat 

Yai train station and hotel in Yala that resulted in the death of a young boy, injuries to 

143 Davis, “Southern Thai Insurgency Gains Fresh Momentum,” 16 – 17.

144 GlobalSecurity.org. “Thailand Islamic Insurgency,” 3 – 4. URL: http://www.globalsecurity.org/

military/world/war/thailand2.htm. Accessed February 1, 2005.
76

several passengers, and severe property damage.145 Blamed by the Thai government on 

PULO, which immediately denied responsibility, Thai authorities appeared unaware 

of the JI insurgent training, planning, and preparations that had been underway in the 

south for several years. 

In his recent book, Imperial Hubris, former lead U.S. Central Intelligence Agency 

analyst on al-Qa'ida, Michael Scheuer, observed that

Since 11 September 2001, the tone of bin Ladin’s rhetoric toward young 

males has changed; where it was once critical and meant to shame 

young men into action, it is now supportive and complimentary. The 

change probably is due to the steady fl ow of young men to the dozen or 

so Islamist insurgencies now being fought in the world...in late 2001, 

[al-Qa'ida] sent fi ghters home from Afghanistan because they were not 

needed in that phase of the war....146

In Scheuer’s analysis, a key purpose of the September 11, 2001, attacks on 

targets in the United States was to inspire Islamist insurgent movements around 

the world, such as those in Thailand, Indonesia, the Philippines, Burma, Kashmir, 

Afghanistan, Chechnya, Xinxiang, Iraq, Saudi Arabia, Yemen, Somalia, Egypt, 

Algeria, etc. If Muslims could attack key nodes of power in the heart of the 

greatest power on earth, the action seemed to say, then surely Muslims engaged 

in even more just causes than the attack on the United States could achieve great 

things in their own areas of operation. 

In the case of southern Thailand, Scheurer’s analysis appears to have merit. 

Although nothing is known about the numbers of Malay Thais that may have returned 

from Afghanistan after the U.S. offensive there in late 2001, the simultaneous largescale arrest of Islamic militants in Singapore, Malaysia, Indonesia, Brunei, and the 

Philippines at this time led many Jemaah Islamiyah suspects throughout southeast 

Asia to fl ee to southern Thailand, where they received safe haven from sympathetic 

elements there.147 Among those fi nding such safe havens was JI leader Hambali who, 

in January 2002, was able to convene a meeting in Bangkok, where planning was 

145 Abuza, 80. Although the train bombing in Yala may have been meant to signal the beginning of the 

renewed insurgency in southern Thailand that actually began in December 2001, the almost concurrent 

arrest of a number of KMM members and general uncovering of that organization in May in neighboring 

Kelantan state may have forced a reappraisal and a delay until conditions were more propitious.

146 Anonymous [Michael Scheuer], Imperial Hubris: Why the West Is Losing the War on Terror 

(Washington, DC: Brassey’s, Inc., 2004), 133 – 134.

147 Anthony L. Smith, “Trouble in Thailand’s Muslim South: Separatism, not Global Terrorism,” in 

Asia-Pacifi c Security Studies, 3, 10 (December 2004), 3. Available online at URL: http://www.apcss.org/ 

Publications/APCSS/Trouble%20in%20Thailands%20Muslim%20South.pdf. Accessed February 1, 2005. 

Although the author of this article still perceives the post-9/11 renewed insurgency in traditional Malay 

separatist terms, he does recognize that the insurgency possessed new elements and that these types of 

“coordinated action[s have] never been so well executed.’’
77

begun for a number of terrorist operations, including the eventual October 12, 2002, 

bombings in Bali, Indonesia.148 What can be said with certainty is that on December 24, 

2001, fi ve carefully coordinated and almost simultaneous attacks on police posts in all 

three Malay provinces of southern Thailand marked the opening strikes of a renewed 

insurgency in southern Thailand that continued unabated, reaching a crescendo of 

insurgent actions during 2004.

Nature of the New Insurgency

The different nature of the renewed insurgency was noted by one commentator:

...up until 2001, separatism and unrest were all but dead in the south. 

Hence the surprise and uncertainty voiced by many Thais, both Muslim 

and Buddhist, to the escalation of violence. Local people appear 

“confused,” as one resident of Yala put it. Senator Aumar Toryib of 

Narathiwat says the local people still don’t know who is behind the 

violence.149

Yet another close observer of the insurgency observed:

In late 2001 GMIP leafl ets scattered in districts of Yala urged holy war 

and support for Osama bin Ladin in the service of the separatist cause...

Beginning in December 2001 and continuing through 2002, a succession 

of assassinations of individual policemen, teachers, local offi cials and 

suspected informers has been punctuated by larger attacks on police 

posts. The pattern has persisted in 2003 along with several incidents that 

seized national attention.

Since they began on 24 December 2001, the attacks have repeatedly 

involved coordinated groups of masked men armed with AK-47 rifl es 

and often mounted on motorbikes, staging near simultaneous attacks 

on widely separated police posts. This suggests a degree of planning, 

tactical competence and aggression that has no precedent in the military 

lacklustre histories of PULO or BRN.150

148 Abuza, 158. Among those present at the meeting were Muklas (Indonesian), Noordin Azari Husin 

(Indonesian), Noordin Mohamad Top (Indonesian), and Wan Min (Malaysian), all of whom were to play later 

important roles in bombings in Indonesia in 2002, 2003, and 2004. International Crisis Group. “Southern 

Thailand: Insurgency, not Jihad,” Asia Report No. 98, 18 May 2005. URL: http://www.crisisgroup.org/

library/documents/asia/south_east_asia/098_southern_thailand_indurgency_not_jihad..pdf. Accessed 

June 6, 2005.

149 Julian Gearing, “Terror in Thailand: ‘Ghosts’ and Jihadis” from Asia Times Online. URL: http://www.

atimes.com/atimes/Southeast_Asia/FD03Ae05.html. Accessed November 2, 2004.

150 Davis, “Thailand Faces up to Southern Extremist Threat,” 13.
78

So clandestine was the nature of the renewed insurgency that analysts and journalists 

commenting on it were somewhat at a loss to account for the new vigor of the antigovernment violence. In a sense, the commentators were only following the analysis 

of the Thai government itself that remained in denial, for a time at least, that it faced 

any more serious challenge than the common criminality to which it had relegated the 

Malay insurgency in the early 1990s. 

Thaksin Finally Reacts

In July 2002, however, Prime Minister Thaksin suddenly reversed his position 

and ordered the Army, Civilian Military Police (CPM 43), and Ministry of Interior to 

reestablish their previously dismantled intelligence apparatus and control headquarters, 

and renamed Southern Border Provinces Peace Building Command (SBPPBC). In 

addition, a coordinating center was established within the Thai National Security 

Council in Bangkok. Although this increased focus on the terrorism problem in 

Thailand led to a number of high-level arrests of JI operatives, including JI operations 

leader, Hambali, on August 11, 2003, the Thai leadership, even in 2004, continued to 

decouple insurgency-related actions in Thailand with “international terrorist groups,” 

including Jemaah Islamiyah.

151

The restored SBPPBC did not immediately cope effectively with the renewed 

insurgency, however. Indeed, almost as if in retaliation for the arrests of Jemaah 

Islamiyah leaders in 2003, the insurgency grew in intensity during 2004. A particularly 

spectacular attack occurred on Sunday, January 4, 2004, in which about 30 Malay 

insurgents attacked a Thai Army post in Narathiwat, killed four soldiers, and seized 

413 fi rearms, including two general-purpose machine guns and a number of rocketpropelled grenade launchers. At the same moment — about 1:30 in the afternoon — other 

insurgents torched 20 government schools and two police posts scattered across 11 

of the 13 districts of Narathiwat province. Other diversions, such as the burning of 

tires on highways and the setting of charges and grenades on bridges, took place 

simultaneously in neighboring Yala province. The operation was well-planned and was 

completed within 20 minutes. Felled trees protected the two trucks used to carry away 

the arsenal of weapons as did scattered nails on all the approach roads to the Army 

post. No fewer than 200 insurgents were estimated to have been required to carry out 

the entire operation, which was obviously most carefully planned and coordinated.152

Although the Thaksin government, recognizing the import of the incident, responded 

by immediately declaring martial law throughout the south, dispatching 3,000 

additional troops to the region, and launching a massive dragnet to arrest individuals 

suspected of being involved in recent acts of insurgent violence, the attention-getting 

151 GlobalSecurity.org, “Thailand Islamic Insurgency,” 3 – 5.

152 Davis, “Thailand Confronts Separatist Violence in its Muslim South,” 20, and Davis, “Southern Thai 

Insurgency Gains Fresh Momentum,” 18, 23.
79

attacks of January 4 proved only the opening shots of a seemingly unending campaign 

of bombings, assassinations, arson attacks, raids aimed at seizing arms, and pin-prick 

attacks on military installations that continued on an almost daily basis throughout 

2004 and into 2005.153

Focusing on the traditional, unlicensed pondoks that government authorities believed 

to be the seedbed of the renewed resistance, they arrested both teachers and students on 

the slightest pretexts, but found such arrests had little impact on insurgent activities.154

On only one occasion, on April 28, 2004, did Thai security forces manage to close in 

on elements of the resistance, when they surrounded some 108 young fi ghters armed 

with knives and a few fi rearms in Pattani’s historic Krue Se mosque and systematically 

killed them all.155 In hindsight, some speculated that for the insurgents the Kreu Se 

“massacre” had been in fact a “suicide operation” designed to highlight the lack of 

respect Thai authorities held for Pattani’s most holy place. The young age of most of 

the dead, the lightness of their arms when in fact hundreds of captured weapons were 

held by the insurgents, the jihadist-related literature found on their persons after their 

deaths, and the cries of “Allahu Akbar” that arose from them as they engaged in the 

fi ght all pointed to this conclusion.156

Although for a few days Thai authorities congratulated themselves on the 

achievement of this victory, it soon became apparent that the incident had no impact 

on the level of violence in southern Thailand. Another unfortunate incident on 

October 24, 2004, held the potential for even further strengthening the insurgency and 

undermining Thai legitimacy in southern Thailand. The death by suffocation of 78 

Muslim men from about 1,300 arrested, after they had been crammed into army trucks 

for a long fi ve-hour drive from Tak Bai in Narathiwat province to the army camp at 

Pattani, affected many families and produced widespread outrage against the security 

forces and the government. The 1,300 men had been part of a crowd of about 2,000 

people that had been demonstrating against the arrest of six men on charges of stealing 

government fi rearms. Over the course of a long day, the crowd had grown and become 

increasingly unruly. Although the Army affi rmed that it had not used live ammunition, 

the bringing of water cannon and tear gas to the scene provoked pandemonium, leading 

to charges of signifi cant police brutality, including nine deaths, as Thai offi cials sought 

to arrest any who resisted them.157

153 Davis, “Southern Thai Insurgency Gains Fresh Momentum”, 17 – 18.

154 Anthony Davis, “School System Forms the Frontline in Thailand’s Southern Unrest,” in Jane’s 

Intelligence Review (November 2004), 10 – 11.

155 Alan Sipress, “Thai Forces Were Ready for Attacks,” The Washington Post, April 29, 2004, A19.

156 Davis, “Southern Thai Insurgency Gains Fresh Momentum,” 14–15.

157 Alisa Tang, “At Least 78 Die after Thailand Riot,” in Northwest Herald Online, October 28, 2004. 

URL: http://www.nwherald.com/MainSection/other/290433813785258.php. Accessed October 28, 2004. 

Marwaan Macan-Marker, “Suffocation Deaths Infl ame Thai South,” Asia Times Online, October 28, 2004. 

URL: http://atimes01.atimes.com/Southeast_Asia/FJ28Ae01.html. Accessed November 2, 2004. Also Alan 

Sipress, “Relatives Seek Bodies of Thai Muslim Demonstrators,” The Washington Post, October 28, 2004, 

A20.
80

The incident, which produced international headlines, provoked outrage among the 

Malay-Muslim population of southern Thailand as well as in neighboring Malaysia, 

where Prime Minister Badawi felt compelled to issue a statement saying, “We hope 

that the situation there [Narathiwat province] does not worsen and spread to other 

provinces and that it will be contained quickly.”158 Only a rash of retaliatory killings 

and bombings followed, however, as the insurgency continued.

Reelection of Thaksin

The massive landslide reelection of Prime Minister Thaksin Shinawatra and his Thai 

Rak Thai (TRT) populist party in the February 5, 2005, elections, in which he gained 

374 out of a possible 500 seats in the Thai parliament, promised to give Thailand a 

degree of political stability the country had not known since the revolution of 1932. 

One area that would remain recalcitrant, however, was the Malay-Muslim south. The 

TRT, which had held six of the 11 parliamentary seats from the three violence-racked 

provinces of Pattani, Narathiwat, and Yala, gained none in the 2005 election.

Indeed, soon after his massive reelection, Thaksin moved quickly to address the 

problem of southern Thailand by establishing a National Reconciliation Commission, 

headed by former prime minister Anand Panyarachun. The stated aim of the commission 

was to soften the policy of the Thai government regarding the southern Muslims in 

an effort to achieve reconciliation by dialogue rather than compliance by force. It 

remained to be seen whether this approach would prove fruitful.159

A Retrospective

In his study of separatist movements in Southeast Asia, Clive Christie notes several 

reasons for their failure in the post-World War II period. Foremost among them has 

been “the general priority given by the states” of the region “to regional stability.” 

Since nearly all states in southeast Asia are “vulnerable to regional discontents and 

separatist impulses” — the Arakanese and Karen in Burma, the Muong montagnards in 

Vietnam, the South Moluccans, the Ambonese and Achenese of Indonesia, the Muslims 

of the Philippines, as well as the Pattani Malay Muslims of southern Thailand-state 

policy in each has generally held aloof from interfering in the “internal” affairs of 

its neighbors. Thus, the UMNO-headed government of Malaysia has refrained from 

supporting the Malay-Muslim cause in southern Thailand, although the minority Malay 

party, PAS, governing Kelantan state, has done so, at least in providing Thai Malay 

Muslim insurgents a safe haven and refuge. In this respect, Christie notes, the “history 

of Southeast Asia since the Second World War has been very different from that of 

158 Anil Netto, “Malaysia Rages over Muslim Killings,” Asia Times Online, October 30, 2004. URL: 

http://www.atimes.com/atimes/Southeast_Asia/FJ30Ae02.html. Accessed November 2, 2004.

159 Marwaan Macan-Markar, “Softly-Softly in Thailand,” in Asia Times Online, 21 May 2005. URL: 

http://www.atimes.com/atimes/Southeast_Asia/GE21Ae01.html. Accessed 3 June 2005.
81

South Asia, where the states of the region have rarely hesitated to exploit the separatist 

diffi culties of their neighbors.”160 In Southeast Asia, the principle of non-interference 

was also enshrined in the 1967 formation of the Association of Southeast Asian Nations 

(ASEAN), whose stated purpose is to foster political stability, regional cooperation, 

and economic development among the member states of the organization.

So too, Christie notes, the United States-led, general international focus on the 

containment of communist movements in the region, not only in Vietnam, placed 

regional separatist movements in a secondary, if not tertiary, position as annoying 

distractions to the far more important Cold War struggle being played out in Southeast 

Asia during the post-World War II period. Separatist movements like that of the 

Malay Muslims of southern Thailand were a source of instability that needed to be 

contained if Thailand were to emerge as a strong and prosperous, Western-oriented 

state capable of resisting the communist threat, both within and on its borders.161

U.S. policy, therefore, contributed to the marginalization of the Malay Muslim issue 

in Thai politics.

The gradual political evolution of most states in the region into “authoritarian 

democracies” — states with democratic processes dominated by a single ruling party, 

such as the UMNO in Malaysia or Golkar in Indonesia, often closely associated with 

the military — placing a stress on rapid economic development, has also been injurious 

to minority views, such as those of the Malay Muslims of southern Thailand, whose 

interests contradict those of the largely Buddhist Thai ruling elite. Unable to achieve 

recognition of their right of self-determination in the immediate post-World War II 

period, their cause has largely been subsumed by “larger” issues. The partial success 

of successive Thai governments, moreover, in achieving at least some degree of 

assimilation of mainly urban members of its Malay Muslim population has also tended 

to undermine the separatist cause, as it was intended to do.

OUTLOOK

Yet, as developments in the post-September 11, 2001, era have demonstrated, the 

cause of Malay Muslim separatism in southern Thailand persists. As Christie notes, to 

some degree the persistence of any separatist movement is strengthened if individuals 

involved in it are closely linked to a historical state, which of course the Muslims 

of southern Thailand are. The fact that Pattani Muslims are on the periphery of the 

Thai state, on the border with ethnically identical Malaysia, rather than located in the 

central part of the state, also contributes to the endurance of Malay Muslim resistance 

to submission to Thai rule. Culturally, despite offi cial Thai assimilationist policies, 

Malays are often referred to by the general Thai public as khaek (foreigners), an 

attitude that generates alienation rather than overcoming it.162 Resistance to Thai rule 

160 Christie, Modern History of Southeast Asia, 195.

161 Christie, Modern History of Southeast Asia, 199–202.

162 Christie, Modern History of Southeast Asia, 192–193.
82

has now endured for more than two centuries and is likely to pose a diffi cult problem 

for Thai authority for many years to come.

When Christie was preparing his study of separatism in southeast Asia during the 

mid-1990s, Pattani Muslim separatism, or “dissidence,” as he prefers to call it, was 

in a quiet phase. “The continuing failure of Patani Malay resistance to achieve its 

separatist goals,” he writes, did not “mean that Thai rule had been accepted in the 

region.” Indeed, he argues, “Patani Muslims have — ever since the Thais began their 

policies of administrative, political, religious and educational integration — attempted 

to live within their own world as if the Thai state did not exist.” This process he 

calls a classic case of “internal hijra, or withdrawal from and non-recognition of kafi r

[infi del] authority.”163

He could not know of the renewed insurgency that was to follow, but he did 

anticipate it by noting the potential for a “resurgence of populism, this time in a 

religious guise.” “Populism” he defi nes as a “process of mass mobilization on the 

basis of ideas, or one fundamental idea, designed to appeal to the prejudices of as 

large a section of the population as possible.” Often, he argues, populist movements 

“have the quality of an overall simplicity of appeal, an inherent ‘anti-elite’ bias, and, 

quite often, a lack of intellectual coherence.”164 “Always hovering in the wings,” he 

notes, “is the possibility that the creation of an Islamic state in Malaysia or a triumph 

of Islamic radicalism in the wider Islamic world might again open up the joint issues 

of Malay and Islamic irredentism in Patani.”165

The perceived triumph of the Islamist-based struggle against the Soviet occupation 

of Afghanistan in the 1980s does indeed appear to have inspired other struggles against 

perceived foreign “occupations” of Islamic lands in other parts of the world. In the 

case of Thailand, although more than a decade was to pass before the renewed struggle 

appeared there, the al-Qa'ida strike against the United States on September 11, 2001, 

appears to have been an igniter of a renewed insurgency in the southern provinces of 

that country.

A key difference between the renewed 21st century Islamist-based insurgency 

and the previous, more nationalist-based insurgency of the 1960s and 1970s was the 

“disturbingly opaque” nature of the confl ict for which “no organization has claimed 

responsibility.”166 Anthony Davis, a close observer of the insurgency in Thailand, 

reached the conclusion that the primary actors in the new insurgency were the old 

pan-Malay BRN, which still maintained a substantial infrastructure in the ThailandMalaysia border area; the GMIP association of veterans of the war in Afghanistan; 

163 Christie, Modern History of Southeast Asia, 189.

164 Christie, Modern History of Southeast Asia, 205–206.

165 Christie, Modern History of Southeast Asia, 190.

166 Davis, “School System Forms the Frontline in Thailand’s Southern Unrest,” 10.
83

and the small but still militant New PULO.167 Whether this was the case or not, the 

actors in the insurgency were a new generation of insurgents that had been engaged in 

planning and training for several years before the outbreak of the insurgency in 2001. 

What was also clear was that, whereas the previous generation had been engaged in a 

“struggle for national liberation,” the new generation was engaged in a jihad, a “give 

me liberty or give me death” type of struggle that was posing a diffi cult challenge for 

the Thai central government.168

167 Davis, “Southern Thai Insurgency Gains Fresh Momentum,” 15.

168 Since these words were penned, the International Crisis Group in Brussels published its study, 

“Southern Thailand: Insurgency, not Jihad,” that reached precisely the opposite conclusion. The author 

leaves it to the reader to compare these two analyses and reach his/her own conclusion. The ICG report, 

which has the benefi t of drawing from police and interrogation reports of captured Islamic militants, is 

rich in detail but perhaps is too cautious in challenging the offi cial policy position of the Thai government. 

Asia Report No. 98, 18 May 2005. URL: http://www.crisisgroup.org/library/documents/asia/south_east_ 

asia/098_southern_thailand_indurgency_not_jihad..pdf. Accessed June 6, 2005.
84

Map of Indonesia.

Source: CIA.
85

CHAPTER 4

ISLAM IN INDONESIA

There will be no reform in Indonesia over the long-term unless Islam is recognized as 

the powerful moral force it is. 

 —Daniel Lev

The politics of the modern, independent state of Indonesia has consisted largely of the 

interactions of an almost exclusively male elite of approximately 2,000 individuals.169

Most of these men are members of the traditional priyayi class, descendants of the 

historic sultans and rajas and their families that were drawn into collaboration with 

the Dutch rulers during the colonial era. In this sense they constitute a continuation 

of the political elite that has governed the Indonesian islands for centuries, whether 

independently in much smaller states, or jointly at the top echelons of a unifi ed, 

independent Indonesia.

Most members of this ruling elite, moreover, are abhangen Muslims, although a 

few are also Hindu, Buddhist, or even Christian. Unlike santri Muslims who strive 

to practice their religion by limiting it to the guidance provided by the Qur’an, the 

hadith, and the Shafi ’i school of Islamic law, abhangen Muslims take a broader view 

and incorporate within Islam religious practices that predate the arrival of Islam in the 

Indonesian archipelago. In general, these practices are referred to as kebatinan, a word 

that relates to the Arabic batin (hidden), that is, the “inner” side of religion (as opposed 

to its external manifestations and requirements). These practices involve ceremonies 

that relate to the spirits that dwell in the kris, the dagger carried by most Indonesian 

men; ceremonies that take note of Semar, the guardian spirit of Java; attention to the 

prophecies of Joyoboyo, an Indonesian counterpart of Nostradamas in the West; and 

ceremonial offerings to Lara Kidul, the Queen of the Indonesian Ocean. Perhaps of 

even greater import is the wayang, or shadow puppet show which unites the traditional 

Hindu Ramayana and Mahabharata epics with fi gures from Islamic history to teach 

about the meaning and purpose of life, of the constant struggle between good and 

evil, and even of transmitting government policies. Constantly staged on birthdays, 

weddings, important religious occasions, or as ritual entertainment during family 

feasts, the wayang is an ever-present aspect of Indonesian abhangen life and a primary 

means of transmitting traditional values from one generation to the next.170

169 Lee Khoon Choy, A Fragile Nation: The Indonesian Crisis (Singapore: World Scientifi c Publishing 

Company, 1999), 7.

170 Lee Khoon Choy, 41 – 147. Lee’s chapter is a detailed and fascinating investigation of “Javanese” 

mysticism (kebatinan) in which the author, Singapore’s ambassador to Indonesia during the early 1970s, 

took a special interest. As Java constitutes approximately 50 percent of the total population of Indonesia, and 

Indonesia may be conceptualized as a Javanese “empire,” inherited from the Dutch who built it, its culture 

and the values associated with that culture tend to be salient in any discussion of Indonesian “culture,” even 

though other islands of the archipelago express cultural norms quite at variance with those of Java.
86

FORMATION OF THE STATE IDEOLOGY

As abhangen Muslims, Indonesia’s dominant political class has tended to identify 

with the Nahdlatul Ulama, the mass movement of Indonesia’s abhangen Muslims, 

established in 1926 in opposition to the more santri-oriented Muhammadiyah. 

Broadly tolerant of religious expression in all its forms, the abhangen elite has not 

only relied on Nahdlatul Ulama as a counterweight to the infl uence of Muhammadiyah 

in Indonesian politics, but also, in the interest of national unity, has held fast to an 

even broader ideological doctrine designed to promote inclusiveness among all of 

Indonesia’s diverse peoples. This is the doctrine of Pancasila, fi rst put forward by 

President Ahmed Sukarno in 1945, and captured in the national slogan inscribed on the 

Indonesian state crest, Bhinneka Tanggut Ika (Unity in Diversity).

Somewhat reminiscent of Sun Yat-sen’s espousal of San Min Chu Yi (Three Peoples’ 

Principles) as the basis for a unifi ed, modernizing, and democratic China, Sukarno’s 

Pancasila enumerated fi ve principles as the basis of governance in Indonesia:

Belief in one God

Humanitarianism

National unity

Representative government

Social justice for all

Pancasila, like the six principles of Atatürkism in Turkey, remains today the offi cial 

guiding ideology of Indonesia. Nevertheless, implementing its principles and ensuring 

its primacy did not come easily and faced many challenges following the declaration 

of Indonesian independence.

The fi rst challenge was the Dutch, who in the late 1940s sought vigorously, though 

unsuccessfully, to reestablish their rule over the East Indies after World War II. 

Following this challenge came that posed by the tendency toward decentralization, 

which threatened to fragment the archipelago into several states. Perhaps even more 

challenging, however, was the Darul Islam movement that denied the legitimacy of 

Pancasila and sought instead the establishment of Indonesia as an Islamic state. Like 

the republican government of Sukarno, however, the Darul Islam movement opposed 

the potential fragmentation of Indonesia and supported the maintenance of its unity.

THE ISLAMIC ALTERNATIVE

During World War II, the Japanese occupation authority had sought to rally Muslim 

opinion against the Western powers by organizing in October 1943 a Consultative 

Council of Indonesian Muslims (Masyumi-Majlis Syura Muslimin Indonesia), that 

sought to unify the Nahdlatul Ulama and Muhammadiyah mass organizations. 

Although Masyumi refused to authorize Muslims to bow toward the Japanese emperor 

and rejected Japan’s request to declare the war against the Allies a jihad, the new 

1.

2.

3.

4.

5.
87

combined organization did collaborate with the occupation authorities and continued 

after the war as one of independent Indonesia’s major political parties. Toward the end 

of the war, as Japan moved increasingly to the defensive, the occupation authorities 

began raising a number of military and paramilitary units to assist in the defense of 

the archipelego. In addition to PETA, the forerunner of the Indonesian Armed Forces 

(ABRI/TNI), Masyumi was also authorized in December 1944 to organize an “Islamic” 

military force which took the name Barisan Hizbullah (Party of God Front).171

Following the surrender of the Japanese, the Hizbullah fought alongside PETA 

against the Dutch, but in 1947 some members of Hizbullah broke away, taking the 

new name Darul Islam (House of Islam) and calling its armed elements the Indonesian 

Islamic Army. Following the Dutch agreement to recognize Indonesian sovereignty 

in December 1949, the Darul Islam based in West Java refused to recognize the 

authority of the new republican government led by Sukarno and proclaimed instead 

an independent Islamic state (Negara Islam Indonesia) in what is now Pasundan 

province. Under the leadership of Soekarmadji Kartosuwiryo, Darul Islam found 

support in Aceh, South Sulawesi, and other areas of the country outside of Java and 

posed a serious insurgency problem for the government until its leader’s capture and 

execution in 1962.172

In addition to these problems and in part because of them, the new government 

remained extremely fragmented for a number of years, with the legislature’s 232 seats 

being divided among many parties. The largest party represented, the Muslim Masyumi, 

had only 49 seats — and that party soon split in 1952, with the more traditionalist 

members of the old Nahdlutal Ulama (NU) recreating their own party.173

Six cabinets were formed in the 1950 – 57 period, refl ecting the constantly shifting 

balance of power between the competing political parties. In addition, Sukarno faced 

a growing challenge from the Communist Party of the Indies (PKI) that dominated 

the powerful Central All-Indonesia Workers Organization (SOBSI) and a rejuvenated 

Indonesian Peasant Front (BNI), as well as more peaceful competition from the social 

democratic Indonesian Socialist Party (PSI). These parties shared his goal of a unifi ed, 

secular, and socialist Indonesia, but were bitterly opposed by the Islamic parties, such 

as Masyumi and the NU, not to mention the Darul Islam. 

Sukarno’s growing impatience with the byzantine complexities of party politics and 

continuing regional and religious unrest led to his decision in 1956 that the democratic 

political process needed to be discarded. In 1957, the military and the PKI both became 

171 William H. Frederick and Robert L. Worden, Indonesia: A Country Study, Department of the Army 

Pamphlet 550–39 (Washington, DC: U.S. Government Printing Offi ce, 1993), 41–42. Also Anthony H. 

Johns, “Indonesia: Islam and Cultural Perspectives,” in Islam in Asia: Religion, Politics, and Society, ed. 

John L. Esposito (New York: Oxford University Press, 1987), 208 – 209.

172 Lee Khoon Choy, 157–158.

173 Indonesia: A Country Study, 49.
88

more dominant players in the economy and control of the nation as the restlessness of 

the outer islands increased. On March 14, 1957, Sukarno declared martial law, ending 

Indonesia’s brief experiment with parliamentary democracy.174 Sukarno referred to his 

new authoritarian approach to governance as “guided democracy,” but he increasingly 

relied on the Army and the PKI (Communist Party) to balance the power of the Islamic 

parties, continuing Dutch infl uence, and regional secessionists.

After a major anti-Sukarno revolt led by civilian and military opponents of the 

President’s growing authoritarianism in February 1958, Sukarno undertook a major 

purge of regional and ideological opponents. Many offi cers from the outer islands were 

forced to resign, leaving the military increasingly Javanese and loyal to Sukarno.175 This 

episode and its aftermath both refl ected and expanded the centralization of politicomilitary control in the hands of the secular Javanese at the expense of both traditional 

Muslims and non-Javanese. Outer island leaders complained of their commoditybased export economies being exploited for the development of import-dominated 

Java. Their complaints were largely ignored until they became violent, at which point 

the Army would suppress them. The growing power of the Army, however, especially 

in the outer islands, increasingly led Sukarno to look to the Java-based Communist 

Party as a means of balancing the increasing power of the military. In August 1960, 

moreover, he formally declared illegal the Masjumi Muslim party, as well as several 

others which had participated in the 1958 revolt against him and refused to submit to 

his concept of “guided democracy.”176

FALL OF SUKARNO

During the “guided democracy” years (1958 – 1965), Sukarno relied on the Army 

and the Communist Party to keep the Islamic parties and regional separatists at bay. 

Increasingly he leaned even more closely on the Communist Party to keep the Army 

at bay. During this period, four other features characterized Sukarno’s style of rule: a 

growing personality cult culminating in his self-appointment as “President for Life” 

in 1963; a sharply deteriorating economy characterized by hyperinfl ation and food 

shortages, as Sukarno spent massive amounts on expensive government buildings, 

public monuments, and military adventurism; a strong foreign policy alignment with 

Beijing, Phnom Penh, Hanoi, and P’yongyang “in order to combat Neocolonialism, 

Colonialism, and Imperialism”; and an aggressive foreign policy aimed at securing 

control of West New Guinea (Irian Jaya under Indonesian rule) from the Dutch in 

1962 and confontation with the new state of Malaysia that had come into being on 

September 16, 1963.177

174 Indonesia: A Country Study, 50.

175 Indonesia: A Country Study, 50, and Sundhaussen, 434 – 438.

176 Indonesia: A Country Study, 51.

177 Indonesia: A Country Study, 51 – 54.
89

Communist Party aggressiveness in enforcing its policies — such as redistribution 

of land to the rural peasantry in areas of the country where it was strong-taking 

advantage of Sukarno’s reliance on the party, provoked hostility in other sectors of 

Indonesian society. The denouement arrived in September 1965 in what came to be 

called the Gestapu coup. Pro-communist offi cers allegedly murdered fi ve generals 

whom they claimed were plotting a coup d’état and seized the Indonesian state radio 

station to announce that fact. If the aim of the involved offi cers was to launch a coup 

d’état of their own, they failed miserably. Other anti-communist Army units under the 

leadership of General Suharto intervened immediately and took charge, ending the 

threat. News of the alleged communist coup d’état provoked a country-wide uprising 

against Indonesian communists, however, and over the next two months literally 

hundreds of thousands of Indonesians alleged to be communists, especially in Jawa 

(East) Timur and on Bali, as well as in parts of Sumatra — all also strongholds of 

traditional separatist sentiment — were killed. Members of the Nahdlatul Ulama’s 

youth branch, Ansor, were particularly active in these mob killings, which targeted 

Indonesia’s wealthy, capitalist Chinese community as well.178

Although Sukarno lived on and technically continued to serve as President of 

Indonesia until his death in June 1970, the liquidation of the PKI and the simultaneous 

purge of pro-Sukarno elements in the Armed Forces had the result of undermining 

his authority and transferring real ruling authority to the Army. Sukarno capitulated 

to the inevitability of his loss on March 11, 1966, when he signed an executive order 

transferring his executive authorities to General Suharto. A year later, on March 12, 

1967, the change of power was carried a step further, when the Provisional People’s 

Consultative Assembly (MPR(S)) recognized Suharto as “Acting President” in place 

of the former President Sukarno.

ASCENDANCY OF THE “NEW ORDER”

Under Suharto, the Armed Forces (ABRI/TNI) came into ascendancy in Indonesian 

politics. Nevertheless, the institutions of republican government remained. Suharto and 

the Army took the view that economic development was the most important objective 

of state policy and treated the anarchic politics that had characterized Sukarno’s rule 

as a disruptive force that needed to be tamed. To do so, Suharto fi rst restructured 

the political party system, forcing the traditional parties to merge into two electoral 

coalitions: the United Development Party (PPP) into which all the Islamic parties 

were required to unite,179 and the Indonesian Democratic Party (PDI) comprising 

the non-Muslim and secular parties. The old PKI (Communist Party of Indonesia) 

was banned.

178 Indonesia: A Country Study, 54 – 57.

179 The four components of the PPP were Nahdlatul Ulama, the Muslim Party of Indonesia (PMI), the 

Islamic Association Party of Indonesia (PSII), and the Islamic Educational Movement (Perti). PMI was a 

resurrected version of the banned Masjumi, a largely santri-oriented party that represented the modernizing 

values of the non-political Muhammadiyah organization. NU and PMI were the dominant partners in the 

PPP. Indonesia: A Country Study, 242 – 243.
90

The centerpiece of his political strategy was the creation by 1973 of a government 

party, Golangan Karya, popularly known as “Golkar,” a coalition of such “functional 

groups” as trade unions, women, and students. Its key component was the bureaucracy, 

as all government workers and offi cials from the capital down to the smallest village 

were expected to be members, and its basic purpose was to serve as “a framework within 

which the military could mobilize civilian support” for its policies.180Throughout the 

duration of Suharto’s rule (1965 – 1998), Golkar succeeded in dominating Indonesia’s 

electoral process, typically controlling approximately 70 percent of seats in the 

National Assembly, elected every four years.

If the Islamic parties felt that Suharto would reward their support in helping to 

overturn the old Sukarno regime, they were wrong in their calculation. Suharto, even 

more forcefully than his successor, reinforced the marginalization of Islam in politics 

by forcing through the parliament in 1984 an act that required every political and 

social organization, including the Islam-based PPP, to proclaim the “civil religion” 

of Pancasila as its “sole ideological principle.” Meanwhile, the government 

crushed opposition by sentencing vocally dissident Muslims to long prison terms 

for subversion. Under Suharto’s rule, the NU, while paying lip service to Pancasila, 

gradually withdrew from the political arena and rededicated itself to strictly religious, 

social, and cultural pursuits.

At the same time, Suharto was not insensitive to the Islamic character of the society 

over which he ruled. As early as February 1968, his New Order government authorized 

the formation of a new Islamic party, Partai Muslimin Indonesia (PMI-Indonesian 

Muslim Party, also known as Parmesi) on condition that no former senior Masyumi 

leaders could occupy leadership positions in it.181 What Suharto seemed to be seeking 

was an Islamic party that would support rather than challenge the legitimacy of the 

state that was based on the principles of Pancasila rather than strictly on shari`a. In 

this case, he was assisted by the emergence of an intellectual trend that began to take 

root during the late 1960s and early 1970s. Centered on individuals associated with 

the Himpunan Mahasiswa Islam (HMI-Islamic University Student Association) and 

Pelajar Islam Indonesia (PII-Islamic Student Association), this intellectual current 

presented a vision of Islam that was quite different from that articulated by the old 

Masyumi leadership or the Darul Islam movement.

Neo-Modernist Islam

Arguing that, although Islam contained a set of socio-political principles, it was 

not an ideology per se, neither was it clear that the Qur’an and the Sunna obliged 

Muslims to establish an “Islamic” state. Moreover, since man was a fallible being 

180 Indonesia: A Country Study, 241.

181 Bahtiar Effendy, Islam and the State in Indonesia. Research in International Studies. Southeast Asia 

Series No. 109 (Singapore: Institute of Southeast Asian Studies, 2003), 45 – 46.
91

incapable of grasping the absolute reality of Islam, the religion was necessarily subject 

to a variety of interpretations, and Muslims therefore were enjoined to be tolerant, 

both of other Muslims as well as non-Muslims, for the benefi t of the community.182

Desirous of ending the historic hostility between the partisans of an “Islamic” state and 

the established political order, this emerging school of thought argued that Muslims 

should accept Pancasila as the overarching ideology of the state, because it permitted 

Muslims to practice their religion freely, as it did other religions in Indonesia.

Being Muslim, however, did not make a man apolitical. Rather, hostility to Pancasila

prevented the Muslim from being engaged politically, whereas acceptance of Pancasila, 

which was deemed by the partisans of the movement to be in accordance with Islam, 

enabled them to be engaged politically and to struggle to “uphold and implement the 

basic principles of Islam within the framework of the Pancasila state.”183

The doyen of this movement was the scholar Nurcholish Madjid, who for 

two consecutive periods (1966 – 1969 and 1969 – 1971) held the position of 

national chairman of the HMI. His views were echoed and supported in a variety 

of ways, however, by a number of scholars in a variety of fi elds, including Dahlan 

Ranuwihardjo, Djohan Effendi, Mansur Hamid, Abdul Wahib, M. Dawam Rahardjo, 

A. Mukti Ali, Harun Nasution, Munawir Syadzani, Ahmad Syafi i Maarif, Amien Rais, 

and Abdurrahman Wahid (later director of Nahdlatul `Ulama (from 1984) and fi nally 

President of Indonesia (1999 – 2001)).184 In many ways, the movement paralleled a 

similar one led by Anwar Ibrahim and the ABIM in neighboring Malaysia during this 

same period, although in this case ABIM (established in 1971) was probably modeled 

after its Indonesian counterpart, HMI (established in 1947). Like ABIM, HMI and 

other similar groups in Indonesia placed an emphasis on study groups, seminars, 

conferences, and other educational venues as a means of raising their and others’ 

Islamic consciousness and thinking about how Islamic values could best be promoted 

in a modernizing Indonesia.

Called by many scholars a “neo-modernist” movement185 whose primary goal was 

to reconcile the values, ethics, and requirements of Islam with the realities of modern 

life by means of vigorous reasoning (ijtihad), its effl uorescence coincided with the general 

trend toward Islamic revival at the societal level throughout the world, including Indonesia, during 

the years following the late 1960s. This was particularly true among the country’s growing urban 

middle class that was expanding rapidly as a result of Suharto’s massive economic development 

schemes. By the mid-1980s, observers universally took note of what they called the growing 

santrifi cation of Indonesian society, particularly among the urban middle class for whom pious 

182 Effendy, Islam and the State in Indonesia, 70.

183 Effendy, Islam and the State in Indonesia, 82.

184 For a brief sketch of the thoughts of many of these individuals, see Effendy, Islam and the State in 

Indonesia, 71 – 80.

185 See, for example, Malcolm Cone, “Neo Modern Islam in Suharto’s Indonesia,” in New Zealand 

Journal of Asian Studies 4, 2 (December 2002), 52 – 67. 
92

observance of religion had become increasingly fashionable.186 Suharto increasingly managed this 

trend by empowering the neo-modernist movement, appointing its most articulate spokesmen to 

high-level government offi ces and leadership positions in Indonesian society. Affi liation 

with the ruling party, Golkar, and collaboration with the ruling regime in support of its 

objectives were, of course, part of this synergy.187

Increased Centrality of Islam under the New Order

Toward the end of the 1980s and early 1990s, the Suharto government undertook 

a number of steps that had the appearance of strengthening the centrality of Islamic 

values in Indonesian political life. Among the steps taken were:188

A new law (March 1989) requiring religious instruction at all levels of statesupported educational institutions.

Enhancing the authority of `ulama-controlled Islamic courts operated by the 

Ministry of Religious Affairs (December 1989), restoring their autonomy 

from the civil courts operated by the Ministry of Justice since the Dutch 

colonial era, and placing both court systems on an equal footing.

The establishment of an Islamic bank (Bank Muamalet Indonesia/BMI) 

(1991)

Lifting the previous ban on wearing of the veil (known as jilbab in Indonesia) 

by women in schools (1991)

Strengthened regulations concerning state management of zakat (obligatory 

alms) (1991)

The founding of an Islamic newspaper, Republika (1992)

Increased Islamic TV programing, including educational programs to teach 

Arabic

Increased state funding for Islamic schools

Termination of the state lottery (1993)

It is impossible to measure the degree to which these steps were adopted as 

concessions to the Muslim majority community of Indonesia or refl ected the growing 

impact of the neo-modernist school on government policymaking or the apparently 

successful model of neighboring Malaysia, where reforms of a similar nature refl ecting 

Islamic values had also been implemented a few years earlier. What is clear, however, 

is that Suharto believed he, like Mahathir Mohammed in neighboring Malaysia, 

could manage this increasing Islamization of Indonesian institutions by relying on 

the leadership provided by the neo-modernist school of Indonesian intellectuals who 

186 See Greg Barton, “The Prospects for Islam,” in Indonesia Today: Challenges of History, ed. by 

Grayson Lloyd and Shannon Smith (Lanham, MD: Rowman & Littlefi eld Publishers, Inc., 2001), 245.

187 Effendy, Islam and the State in Indonesia, 151 – 154.

188 Abuza, Militant Islam in Southeast Asia, 64 – 65. Effendy, Islam and the State in Indonesia, 

154 – 167.

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93

strongly believed in the possibility of combining traditional Islamic values with 

modern modes of life within the context of the state ideology of Pancasila.

To this end Suharto in 1990 created a new state-controlled organization, the 

Association of Muslim Intellectuals (ICMI), to serve as a central focal point, 

research center, and distributor of information for neo-modernist ideas about Islam 

and its relation to the Indonesian state. Headed by his close associate, B. J. Habibie, 

whom Suharto later designated his Vice President and who succeeded him briefl y as 

President following his fall from power in May 1998, the ICMI was designed to be a 

center for authoritative interpretation of Islam as well as a venue for discussion about 

an Islam that was perceived to be deeply imbedded as part of the cultural fabric of 

Indonesia but irrelevant politically in a depoliticized Pancasila-based state. Although 

some have argued that Surharto’s “turn toward Islam” during this period, highlighted 

by his own well-publicized pilgrimage to Mecca in 1991, was designed to balance 

weakening support for him within the military, his traditional base of political support, 

it also seems true that he was seeking to implant permanently a vision of Islam that 

recognized the religion’s salience in Indonesian society, yet which also could not be 

construed as offensive by the Christian, Hindu, and Buddhist minorities of Indonesia. 

The synergy achieved led some outside observers to view Indonesia in the last years 

of Suharto’s New Order as one of the “most vibrant centers for new Muslim political 

thinking the modern world has seen.”189

Conservative Reactions to Neo-Modernism

The growing ascendancy of “neo-modernist” Islam in Suharto’s Indonesia did not 

go unchallenged, however. The leading opposition movement to the neo-modernists, 

as well as Suharto, was the Dewan Dakwah Islamiyah Indonesia (DDII). Established 

as early as February 1967 by former Masyumi party leaders who were disgruntled 

by Suharto’s opposition to them, despite their support for his coup d’état against 

Sukarno and liquidation of Indonesia’s communist movement, its most prominent 

spokesman was Mohammed Natsir (d. 1993), whom one writer has characterized as 

“the most charismatic puritan Muslim leader there ever was.”190 Ostensibly devoted 

to Islamic proseletyzing rather than politics, Natsir and his colleagues expressed the 

view that recent history indicated that Indonesians were not yet ready to constitute 

an Islamic state. Impressed, but also gravely concerned, by the apparent success of 

Christian, especially Catholic missionaries, at gaining converts, particularly in former 

Communist stronghold areas, they decided to devote their organization to dakwah

189 Robert Hefner, “Indonesian Islam in a World Contest,” paper presented at a joint conference 

sponsored by the United States-Indonesia Society and the Asia Society, Washington, DC, 

February 7, 2002, 4. Available at URL: http://www.usindo.org/miscellaneous/into-us_conf.pdf. Accessed 

April 7, 2005.

190 Martin van Bruinessen, “Genealogies of Islamic Radicalism in post-Suharto Indonesia,” online 

article posted by the author on the University of Utrecht website. URL http://www.let.uu.nl/~martin. 

vanbruinessen/personal/publications/genealogies_islamic_redicalism.html. 
94

(du’a — Islamic evangelism) in order to encourage Indonesia’s Muslims to be “better” 

Muslims and also to combat Christian evangelism. Another feature of Dewan Dakwah, 

particularly in light of the 1967 Arab-Israeli war, was a strong orientation toward 

the Middle East, and Saudi Arabia in particular. In 1962, the Saudis had established 

the Islamic World League (Rabitat al-`Alam al-Islami), and Natsir, who eventually 

became one of its vice presidents, was able to gain recognition for his organization as 

the principal operating arm of the League in Indonesia. This status, of course, brought 

with it signifi cant sources of funding and broad international connections with likeminded groups elsewhere in the Islamic world.191

Regardless of its overtly apolitical stance, the DDII remained a principal focal 

point of opposition to the Suharto regime and most of its policies. Although most 

of its leaders had their roots in the modernist Muhammadiyah movement and the 

old Masyumi party, in their new form they adopted a more conservative and even 

paranoid outlook, holding that the end result of the Suharto government would be the 

destruction of Islam in Indonesia. Refl ecting the support it received from Saudi Arabia 

and allied oil-rich states, such as Kuwait, the DDII fi ercely opposed Shi`a teachings 

as it also did those of the neo-modernists who were fi nding favor with the Suharto 

regime. Both were perceived as threats to Islam, as were also the alleged activities of 

191 Van Bruinessen, “Genealogies,” 4. Also Peter Symonds, “Political Origins and Outlook of Jemaah 

Islamiyah,” Part 2, 2. World Socialist Web Site. URL http://www.wsws.org/articles/2003/ nov2003/ji2_n13.

shtml. Accessed 6 May 2005. Also Barton, “Islam and Politics in the New Indonesia,” 50.

Close-up view of Borobuder Buddhist Temple in Yogyakarta, Java, Indonesia, September 2000.

Source: NGA Research Center — Ground Photography Collection.
95

Jews and both foreign and domestic Christians, tolerance of whom was the primary 

basis for upholding the doctrine of Pancasila.

192 Unable to act politically, the DDII 

remained primarily a preaching and educational movement, but it kept alive a climate 

of hostility to the Suharto government that would eventually bear fruit in the collapse 

of the regime in May 1998.

SURVIVAL AND REVIVAL OF DARUL ISLAM

The degree of collaboration between the DDII and continuing militant groups 

remains unclear, but groups more militant than the DDII continued to make their 

presence felt throughout the Suharto years, despite fi erce efforts of the government’s 

security organs to contain them. Although it was militarily crushed in 1962, with its 

top leadership either executed or imprisoned, the Darul Islam movement, which had 

challenged the legitimacy of Sukarno’s nationalist, republican movement from the 

beginning, survived, albeit underground, and continues to be active today.193 Indeed, 

although aware of its existence and determined to crush it once and for all, the Suharto 

government unwittingly played a role in breathing new life into the movement almost 

from the beginning. In the wake of the failed, so-called communist-led Gestapu

coup that brought Suharto to power, the new leader through his intelligence chief, 

General Ali Murtopo, provided arms to a number of former Darul Islam cadres in 

exchange for their help in attacking communists in the areas where they lived. For 

their part, some Darul Islam leaders saw it to their advantage to collaborate with 

192 Van Bruinessen, “Genealogies,” 7.

193 A detailed examination of the underground Darul Islam movement after 1962 is provided by the 

International Crisis Group (ICG), Recycling Militants in Indonesia: Darul Islam and the Australian 

Embassy Bombing. ICG Asia Report No. 92, February 22, 2005. Available at http://www.crisisgroup.org/

library/documents/asia/indonesia/092_recycl_militants_indon_darul-islam_austr_embassy_bombing.pdf. 

Unless otherwise noted, the discussion here follows this ICG report.

View from the base of Borobuder Temple in Yogyakarta, Java, Indonesia, September 2000.

Source: NGA Research Center — Ground Photography Collection.
96

the government both to weaken the communist movement in Indonesia and to relieve 

pressure on themselves.

Murtopo, who had been an original member of Hizbollah, but had joined the 

PETA following the 1947 split between the two organizations, was in fact engaged 

in a double game. Gradually he encouraged the revival of Darul Islam, but mainly 

to gain information about its membership and to direct its activities to support of 

government purposes.194 The Darul Islam leaders, however, were collaborating with 

the government in order to bide time until they could reestablish their organization. 

In 1974, the up-to-now highly fragmented Darul Islam managed to reforge a unifi ed 

organization, and in 1976 began to undertake military (terrorist) operations under the 

name of a newly formed operations group, Komando Jihad. From this time until the 

mid-1980s, Indonesia was beset by repeated instances of “Islamic” terrorism-arson 

and bombing of churches, nightclubs, and cinemas-that usually were attributed in 

the press to an unknown group called Komando Jihad. The violence associated with 

Komando Jihad, however, tended to coincide with election campaigns, as if violence 

would persuade voters to vote for the single Muslim party, the PPP. It, of course, had 

the opposite effect.195

Government collaboration with the Komando Jihad was in fact a “sting” operation, 

and in mid-1977 the Suharto regime arrested 185 people, mostly individuals with longtime Darul Islam connections, whom it accused of constituting the Komando Jihad

organization. The government action did not halt the pattern of violence, however. 

What government offi cials had failed to recognize was that the revival of Darul Islam

tapped into the emerging Islamic “intellectual ferment that was particularly pronounced 

in university-based mosques. That ferment was only beginning when Komando 

Jihad was created, but through the late 1970s and early 1980s it was fueled by the 

Iranian revolution, the availability of Indonesian translations of writings on political 

Islam from the Middle East and Pakistan; and anger over...government policies.”196

Among the sources of this anger was the government sting operation itself. One of 

those arrested in the 1977 dragnet was the father of Fathur Rahman al-Ghozi, later a 

key Jemaah Islamiyah operative, active in the Philippines.197 To some in the younger 

generation, the Komando Jihad proved to be a source of inspiration, strengthening the 

movement with new recruits, as well as providing evidence of the perfi dious nature of 

the ruling regime.

194 Some have argued that Murtopo’s real agenda was to build a force that would enable him to “neutralize 

Suharto and raise himself to the presidency. In return, he had promised support to the goals of Darul Islam

in the event he became President.” International Crisis Group, Recycling Militants, 6, fn 24. If this was the 

case, he was outmaneuvered by Suharto, who used the inside knowledge gained of the organization and 

structure of the revived Darul Islam in a determined effort to crush the movement permanently.

195 Van Bruinessen, “Genealogies,” 7.

196 International Crisis Group (ICG), Al-Qaeda in Southeast Asia: The Case of the Ngruki Network in 

Indonesia, ISG Indonesia Briefi ng, Jakarta/Brussels, August 8, 2002, 8 – 9. Available at URL: http://www.

crisisgroup.org/library/documents/report_archive/A400733_08082002.pdf. Accessed April 13, 2005.

197 International Crisis Group, Ngruki Network, 9.
97

Among those caught up in the follow-up arrests of the Komando Jihad liquidation 

operation were two Islamic scholars, Abdullah Sungkar and Abu Bakar Ba’asyir, 

founders of the religious school Pondok Ngruki, near Solo (Surakarta) in central 

Java, and who later would establish the Jemaah Islamiyah organization in Malaysia. 

Accused, tried, and convicted of being initiated members of Darul Islam, despite their 

protestations to the contrary, the charges against these two men do indeed appear to 

have been fabricated, although the two men were supportive of the goals of Darul 

Islam and were acquainted with its leaders.198 Rather they were active leaders of 

the DDII and were closely associated with DDII leader, Muhammad Natsir. This 

was especially true of Sungkar, who had been an active fi gure in the now defunct 

Masyumi party and a close associate of Natsir. Some have argued that the charges 

against Sungkar and Ba’asyir at this time were aimed at associating the DDII with 

the violence of Komando Jihad and the Darul Islam movement. Whatever the case, 

Natsir and the DDII remained strong supporters of Sungkar and Ba’asyir, even during 

their period of exile in Malaysia, when after 1985 the DDII and the Rabitat al`Alam 

al-Islami, of which Natsir was a vice president in Indonesia, were the principal sources 

of funding for the several hundred Indonesian fi ghters that were sent through Malaysia 

to Pakistan to receive military training and to provide support to the Afghan resistance 

to the Soviet occupation of Afghanistan.199

As active leaders of the DDII — Sungkar was chairman of the DDII Central Java 

Branch — Sungkar and Ba’asyir, together with another, Hasan Basri, in 1967 established 

a radio station called Radio Dakwah Islamiyah Surakarta (Islamic Proselytization 

Radio Surakarta/Solo) that remained on the air until closed down by the government 

in 1975 because of its anti-government tone. Meanwhile, in 1971 the two men also 

established Pesantren al-Mu’min, which in 1973 they moved to the village of Ngruki, 

outside of Solo, after which time it gradually came to be called Pondok Ngruki.200 In 

later years, this school would gain fame as a principal recruiting ground for young 

recruits being sent to Afghanistan and in the 1990s for being the alma mater of many 

associated with the militant Jemaah Islamiyah movement.

Arrested on November 10, 1978, for alleged involvement with Komando Jihad

and the Darul Islam movement, Sungkar and Ba’asyir were fi nally tried and found 

198 In its 2005 report on Darul Islam, the International Crisis Group stated that “Achmad Hussein, 

from Kudus, Central Java, and Hispran [Haji Ismail Pranoto] from Surabaya...formally inducted Abu Bakar 

Ba’asyir and Abdullah Sungkar into DI in 1976.” International Crisis Group, Recycling Militants, 11. In its 

earlier 2002 Ngruki Network study, 7, the same authors had noted that “while Sangkar and Ba’asyir were 

never part of the original Darul Islam, they were deeply sympathetic to its aims,’’ but that “the government 

charged [during their trial] that in 1976, Hispran inducted them into Darul Islam by having them swear an 

oath used in 1948 by Kartosuwirjo.” The earlier charge is well-documented by the authors, whereas the 

latter is not. Whether formally “inducted” or not, the very least one can say is that they were implicated by 

association because of the moral support they lent to Darul Islam and the close relationship they had with 

some of its members.

199 International Crisis Group (ICG), Jemaah Islamiyah in South East Asia: Damaged but Still 

Dangerous, ICG Asia Report No. 63, August 26, 2003, 3. Available at URL: http://www.crisisgroup.org/ 

library/documents/report_archive/A401104_26082003.pdf. Accessed April 13, 2005.

200 International Crisis Group, Ngruki Network, 6 – 7.
98

guilty of many anti-government activities in 1982 and sentenced to nine years in 

prison. Released on appeal in late 1982, they returned to Pondok Ngruki for the next 

two years until, learning of their imminent rearrest in February 1985, they secretly 

fl ed to Malaysia. The rearrest order for Sungkar and Ba’asyir was part of yet another 

crackdown that had followed heightened Islamic opposition across the country to 

Suharto’s May 1984 requirement that all organizations adopt Pancasila as their “sole 

ideological basis.” Although the main Muslim organizations, Muhammadiyah and 

Nahdlatul Ulama, formally accepted this requirement, many other smaller Islamic 

organizations did not and engaged in protest demonstrations against the new law.

A particularly bloody confrontation occurred in September 1984 in the Tanjung 

Priok port area of Jakarta, in which government forces fi red on and killed dozens 

of Muslim protesters (rioters). The Tanjung Priok “massacre,” as it came to be 

remembered, signaled the beginning of an even more intense period of confl ict 

between the government and militant Muslim groups that included several bombings 

and other acts of violence in which a number of fi gures associated with Pondok Ngruki 

were implicated. Among these were a Christmas Eve 1984 church bombing in Malang 

and another major bombing of the recently restored Borobodar Buddhist temple on 

January 21, 1985.201 Also hit were several branches of a major bank owned by one of 

President Suharto’s Chinese business partners.202

The fl ight of Sungkar and Ba’asyir along with others203 to Malaysia did not mean 

an end to confl ict in Indonesia, however. A 1989 bloody shootout at a Muslim school 

in Way Jepara, Lampang, like Tanjung Priok, became yet another in a growing list of 

Muslim grievances against the Suharto government.204 Still, massive arrests and rigged 

trials of virtually anyone who could be associated with dissent against the regime had 

a certain quieting effect in the early 1990s.205 This was also the period when Suharto 

began to adopt the variety of measures, noted above, that tended to recognize the 

centrality of Islamic values for most Indonesians, albeit only within the context of the 

“neo-modernist” understanding of Islam that supported the doctrine of Pancasila upon 

which the state was based. 

Islamists in Disarray

For its part, the Islamic opponents of the regime were entering a period of disarray 

that refl ected leadership struggles as well as differences concerning long- and shortterm goals and objectives. Although the goal of all remained the establishment of 

201 International Crisis Group, Ngruki Network, 8 – 9, 15.

202 Van Bruinessen, “Genealogies,” 8.

203 Among those who traveled with the two leaders were Fikiruddin, Agus Sunarto, Ahmad Fallah, Rusli 

Aryas, Mubin Bustami, Fajar Sidaq, and Agung Riyadi. ICG, Ngruki Network, 11.

204 International Crisis Group, Ngruki Network, 15.

205 Van Bruinessen, “Genealogies,” 8.
99

Indonesia as an Islamic state in which the shari`a, administered by the `ulama, would 

prevail as the characteristic law of the state, there were differences in approach about 

how to achieve this end. Put most simply, the split was between those called fi llah

(with God) and those called fi sabilillah (in the way/path of God). To the latter, jihad

(struggle in the way/path of God — fi sabilillah — including military actions) was a 

continuing requirement of God and the shari`a that was incumbent on every Muslim 

and could not be set aside or postponed for a later time. For the former, Indonesia was 

simply a society that was not yet ready for a military struggle to be successfully waged 

in the short term. What was necessary was to work through dakwah (proselytization) to 

build up a stronger Islamic society (jemaah islamiyah) that would eventually become 

the basis of a mass movement that the secular, nationalist, and authoritarian Pancasila

regime could no longer resist. The approach of the fi llah refl ected the infl uence of 

Natsir’s DDII, yet much to the consternation of the fi sabilillah, the fi llah considered 

themselves part of Darul Islam, while refusing to accept the fi sabilillah leadership.206

The fi llah movement within Darul Islam also refl ected the model of the Muslim 

Brotherhood (al-Ikhwan al-Muslimin) in Egypt and the teachings of its founder, 

Hasan al-Banna. Although both the Egyptian Muslim Brotherhood and the Indonesian 

Muhammadiyah organization had grown out of the Islamic modernist reform movement 

articulated in the late 19th and early 20th centuries by the modernist thinkers, Jamal alDin al-Afghani, Muhammad Abduh, and Rashid Rida, the Muhammadiyah, much more 

effectively than the Muslim Brotherhood, had retained the modernist spirit advocated 

by the reformers, funding schools that trained students in modern technical subjects as 

well as providing them with a strong santri-oriented religious education. As a result, 

Muhammadiyah graduates were generally more effectively prepared to obtain employment 

in the modern sector of Indonesia’s government and economy than graduates of schools 

operated by the Nahdlatul `Ulama, who received a more traditional abhangen-oriented 

religious education. Although Indonesia, therefore, remained dominated politically by 

the abhangen Islamic religious tradition, its mid-level professional sector tended to be 

fi lled with santri Muslims from the Muhammadiyah schools.

In Egypt, by contrast, the Muslim Brotherhood had rapidly lost its original modernist 

character and evolved into an organization championing a more orthodox form of 

traditional Islam.207 It nevertheless had been successful in growing into a large mass 

organization. One of the apparent secrets of its success, adopted by the promoters of 

the fi llah movement within Darul Islam, was al-Banna’s recruitment method known as 

usroh (literally family). The concept was to gather together small groups of ten to fi fteen 

people who committed themselves to live together in accordance with the requirements 

of Islamic law. Such groups were fundamentally study groups that together undertook a 

directed program of instruction that culminated in the group’s induction into Darul Islam

at a graduation ceremony.208

206 International Crisis Group, Recycling Militants, 10 – 11.

207 For an interesting comparative analysis of the two movements, see Giora Eliraz, Islam in Indonesia: 

Modernism, Radicalism, and the Middle East (Portland, OR: Sussex Academic Press, 2004), 1 – 25.

208 International Crisis Group, Recycling Militants, 12.
100

Although the fi sabilillah sector of Darul Islam strongly disparaged the “passive” 

activities of the fi llah group, the usroh proselytization activity gave new energy and a 

sense of purpose to those activists engaged in it, and the usroh movement fl ourished in the 

1980s and 1990s, whereas those associated with the fi sabilillah group were increasingly 

driven underground in the face of government efforts to liquidate the movement. The 

fi llah activists were no less fervent in their opposition to the Suharto regime, however, 

than their fi sabilillah counterparts. Strongly infl uenced by the example of the 1979 

Islamic revolution in Iran, they viewed Suharto as Indonesia’s Shah. At some point, 

due to mass pressure resulting from his autocracy, he would fall. At such a time, it was 

necessary for Indonesian society to be structured as a true jemaah islamiyah. As in Iran, 

under an effective leader like Khomeini, a strong jemaah islamiyah would enable an 

Islamic state to be proclaimed.209

Preparation at Pondok Ngruki

Although the usroh movement had a number of centers, one of the important ones 

was the Ngruki school of Abdullah Sungkar and Abu Bakar Ba’asyir.210 Al-Banna’s 

manual, translated into bahasa Indonesia, was a standard text in Pondok Ngruki.211

So also was another work by a Ngruki faculty member, Abd al-Qadir Baraja. His 

work, Jihad and Hijrah, was considered subversive by the Suharto regime, and use of 

it in Pondok Ngruki was one of the charges brought against Sungkar and Ba’asyir at 

their 1982 trial.212 Again drawing on the example of militant elements of the Egyptian 

Muslim Brotherhood, Baraja argued that successful jihad had to be preceded by a 

hijrah (migration), following the Prophet’s example of fi rst migrating from Mecca to 

Madina, where he was able to create a strong jemaah islamiyah prior to successfully 

confronting his enemies in Mecca. Such a migration could be an internal, spiritual one 

in which the believer separated himself from the corrupt society surrounding him213

and associated himself with an usroh group, where a pure Islamic life based on the 

shari`a could be lived. It could also be a literal migration, such as Muhammad’s hijrah

to Madina, or Ayatollah Khomeini’s more recent exile from Iran. Both Sungkar and 

Ba’asyir interpreted their decision to evade arrest in February 1985 and escape to 

Malaysia as just such a hijrah.

214 There was much work to be done, however. Both 

clearly expected to return to Indonesia one day-if God willed it-as Khomeini had in 

Iran and Muhammad in Mecca, as the leaders of a movement that would fi nally achieve 

the objective of Darul Islam — the transformation of Indonesia into an Islamic state.

209 For the full discussion of the “Iran model,” see International Crisis Group, Recycling Militants, 

13 – 14.

210 International Crisis Group, Ngruki Network, 9 – 10.

211 Usroh serta Pedoman Penyelenggaraan Grup Studi dan Diskusi Usroh [Usroh and a Guide for 

Implementing Usroh Study and Discussion Groups]. International Crisis Group, Recycling Militants, 12.

212 International Crisis Group, Ngruki Network, 15.

213 In Islamic terminology, such a separation is called takfi r (declaration of the corrupt, surrounding 

society as infi del — kafi r), even though most of its members are ostensibly Muslims. Sometimes translated 

into English as “repentance,” takfi r is a stronger word that implies more than just turning oneself away from 

the corrupt society in which one lives, but actually condemning that society.

214 International Crisis Group, Ngruki Network, 11.
101

Soon after arriving in Malaysia, both Sungkar and Ba’asyir travelled to Saudi 

Arabia to solicit fi nancial support, and at the same time “decided to strengthen the 

jemaah militarily by sending volunteers from Jakarta to train in Afghanistan.”215

Saudi agreement to provide such funding was obtained, but apparently only through 

the Rabitat al-`Alam al-Islami offi ce in Jakarta and Natsir’s DDII. For local support, 

Sungkar found sympathetic Malaysian businessmen who agreed to employ a number 

of Indonesian workers brought over in return for agreement to provide twenty percent 

of their salaries to support the organization he was building. Donors in Indonesia also 

remained important sources of income for Sungkar and Ba’asyir.

Although in exile in Malaysia, Sungkar continued to maintain close contact with 

colleagues in Indonesia, primarily through couriers, and as an institutional base he 

and Ba’asyir established a new school in Johor called Pondok/Pesantren Luqmanul 

Hakiem.

216 This school, presumably a clone of Pondok Ngruki in Solo, became a 

halfway house for young recruits prior to their being sent on to Pakistan/Afghanistan, 

or simply as a place of refuge for Islamic opponents of the Suharto regime.217 The 

gradual preparation of a well-trained network of supporters to serve eventually as 

the vanguard of an Iranian-style Islamic revolution in Indonesia following the fall 

of Suharto was the primary aim of Sungkar’s and Ba’asyir’s organizational efforts 

in Malaysia, however. For this purpose, the program of sending young recruits to 

Pakistan and Afghanistan to receive mujahidin training was central.

The Role of Afghanistan

In its August 2003 study, Jemaah Islamiyah in Southeast Asia: Damaged but Still 

Dangerous, the International Crisis Group, relying on police reports and personal 

interviews with arrested Jemaah Islamiyah operatives, accomplished the remarkable 

feat of detailing who many of the Indonesian recruits sent to Pakistan, beginning in 

1985, were.218 That more Indonesians went to Pakistan/Afghanistan than just those 

sent by Sungkar is also apparent from the observation that when the fi rst cadres of 

Filipino Moro Islamic Liberation Front (MILF) fi ghters arrived at Afghan resistance 

leader Abd al-Rasul Sayyaf’s Camp Saadah in Parachinar, Khurram Agency, Pakistan, 

215 International Crisis Group, Ngruki Network, 12.

216 International Crisis Group (ICG), Indonesia Backgrounder: How the Jemaah Islamiyah Terrorist 

Network Operates. ICG Asia Report No. 43, December 11, 2002, 3. URL: http://www. crisisgroup.org/

home/index.cfmid=6686516&CFTOKEN=17890206. Accessed April 20, 2005.

217 One example of an attendee of Luqmanul Hakiem who was not among those sent on to Pakistan was 

Amrozi, arrested in November 2002 for involvement in the October 2002 bombing of the Sari nightclub 

in Bali. One of those workers brought over from Indonesia in late 1985 to work for six months with a 

Malaysian employer, he returned to Malaysia in 1992 to study at Sungkar’s school in Johor, where he 

remained until 1997. International Crisis Group, How Jemaah Islamiyah Operates, 3, 31.

218 International Crisis Group (ICG), Jemaah Islamiyah in Southeast Asia: Damaged but Still 

Dangerous. ICG Asia Report No. 63, August 26, 2003, 4 – 10. URL: http://www.crisisgroup.org/home/ 

index.cfmid=1452&l=1. Accessed April 20, 2005.
102

for training in 1985, they found Indonesian instructors among their trainers.219 Indeed, 

according to Pakistani journalist Ahmed Rashid, Southeast Asians had been training 

in Pakistan and Afghanistan at least as early as 1982.220 With the arrival of Sungkar 

and Ba’asyir in Malaysia, however, this program of recruitment and training took on 

clearer form and organization.

Little specifi c evidence exists detailing the degree to which Sungkar and Ba’asyir 

also took over the recruitment and travel arrangements of volunteers for Afghanistan 

from elsewhere in Southeast Asia, specifi cally Malaysia itself, southern Thailand, and 

the southern Philippines. In light of subsequent developments, it is clear that they 

became a key node for this traffi cking. In Pakistan as well, all Southeast Asians were 

grouped as one qabilah (Arabic for tribe) at Camp Saadah. Another qabilah grouped 

Arabs from Saudi Arabia, Egypt, and Jordan, while yet a third qabilah grouped 

volunteers from North Africa, largely Algerians and Tunisians. There reportedly was 

little contact or interaction among the separate qaba’il (plural of qabilah).221

FORMAL ESTABLISHMENT OF JEMAAH ISLAMIYAH

The involvement of Sungkar and Ba’asyir in this larger effort led to an evolution 

in their own sense of mission. Evidence of this change became apparent in a 1988 

meeting in Pakistan in which Sungkar and Ba’asyir had arranged for the Darul Islam

leader, Ajengan Masduki, to observe mujahidin training at Camp Saadah and to meet 

Abd al-Rasul Sayyaf as well as the Maktab al-Khidmat director, Abdullah Azzam. 

Fluent in Arabic, which Masduki was not,222 Sungkar conducted the meeting as if he 

rather than Masduki was the true spiritual leader of Darul Islam and that Darul Islam

was now a movement throughout Southeast Asia and not solely confi ned to Indonesia. 

A growing split between the two men became increasingly evident, as Masduki and 

those loyal to him raised complaints about Sungkar’s alleged misappropriation of 

funds for Afghanistan training and his insistence that new recruits swear loyalty (bai`a) 

to himself rather than to the Darul Islam organization and remain under his control 

after returning from Afghanistan, whether settling in Malaysia or Indonesia. The split 

became fi nal when, on January 1, 1993, Sungkar and Ba’asyir formally established 

the Jemaah Islamiyah organization. One manifestation of this “split was that all the 

students at Pondok Ngruki whose parents were Masduki loyalists moved to another 

pesantren, Nurul Salam in Ciamis.”223

219 International Crisis Group, “Southern Philippines Backgrounder: Terrorism and the Peace Process” 

(Singapore/Brussels: ICG Asia Report No. 80, July 13, 2004), 14. URL: http://www.crisisgroup. org/home/

index.cfm?id=2863&l=1. Accessed April 13, 2005.

220 International Crisis Group, Damaged but Still Dangerous, 3, fn. 13.

221 International Crisis Group, Damaged but Still Dangerous, 5.

222 Both Sungkar and Ba’asyir were Indonesians of Hadramati (South Yemeni) origins for whom Arabic 

was a native language. They were part of a large Hadramati immigrant community in Indonesia. On their 

historic role as cross-cultural brokers between Indonesia and the Muslim Arab world, see Eliraz, Islam in 

Indonesia, 48 – 52.

223 International Crisis Group, Recycling Militants, 22.
103

As detailed elsewhere in this study,224 the formal establishment of Jemaah Islamiyah

followed another meeting in Pakistan in late 1991 between Sungkar and al-Qa'ida

leader Usama bin Ladin, following the latter’s break with the royal family of Saudi 

Arabia over its decision to request U.S. troops to enter Saudi Arabia to confront Iraq’s 

August 2, 1990, invasion and occupation of Kuwait. In light of subsequent events, 

it is clear that at this meeting bin Ladin agreed to take over the fi nancing of further 

mujahidin training of Southeast Asians in Afghanistan. The decision to establish 

a formally structured Jemaah Islamiyah organization in Southeast Asia, closely 

paralleling bin Ladin’s own al-Qa'ida, also appears to have dated from this meeting. 

So also did the establishment of the group in the Philippines that soon would be called 

the Abu Sayyaf Group (ASG).225

Yet another decision appears to have been Jemaah Islamiyah agreement to provide 

safe haven and logistical support to al-Qa'ida operatives planning and/or executing 

military (terrorist) operations against Western interests in the Southeast Asia region. 

On this basis the groundwork was laid for OPLAN Bojinka, the al-Qa'ida operation 

accidentally foiled by Philippine security forces in January 1995 that had had as its 

aim the potential assassinations of Pope John Paul II, U.S. President Bill Clinton, 

and the blowing up over the Pacifi c Ocean of up to eleven U.S. commercial aircraft 

planned for sometime in early 1995. Supported by Jemaah Islamiyah operatives in 

Malaysia, OPLAN Bojinka was an entirely al-Qa'ida operation, despite a telephone 

call from operation leader Ramzi Yousef to the Associated Press claiming credit for 

the Abu Sayyaf Group.226

Goals of Jemaah Islamiyah

Little actually is known about the formative years of Jemaah Islamiyah, although 

new information constantly comes to light as various members of the organization are 

apprehended, interrogated, and tried. The organization, offi cially established on January 

1, 1993, operated with the utmost secrecy, and it was not until the December 2001 

arrests of 15 individuals in Singapore and another 15 in Malaysia that knowledge of 

Jemaah Islamiyah’s existence became known. The arrests, moreover, only occurred as 

the result of a tip-off from U.S. authorities who had discovered a surveillance videotape 

in Afghanistan that indicated planning for terrorist attacks against the U.S. presence 

and personnel in Singapore. Found in the rubble of a house in Kabul that had been 

inhabited by al-Qa'ida leader Muhammad Atef, the videotape indicated surveillance 

of potential U.S. military, commercial, and diplomatic targets in Singapore and a clear 

linkage between the al-Qa'ida leadership in Kabul and individuals in Singapore and 

224 See above, Chapter 2, 45.

225 See below, Chapter 6, 202-203.

226 Simon Reeve, The New Jackals: Ramzi Yousef, Osama bin Ladin and the Future of Terrorism (Boston: 

Northeastern University Press, 1999), 80.
104

Malaysia. Interrogation of those arrested in Singapore and Malaysia revealed the 

existence of Jemaah Islamiyah.

227

By the time of these arrests, however, Sungkar, Ba’asyir, and other elements of 

the organization had returned to Indonesia following the fall of the Suharto regime 

in May 1998. In the chaotic political environment that emerged after Suharto’s fall 

from power, the Jemaah Islamiyah leadership clearly hoped to lead the long hoped 

for Islamic revolution in Indonesia, as had Ruhollah Khomeini in Iran two decades 

earlier. As a result, the portrait drawn of Jemaah Islamiyah as it was developing in the 

1990s was signifi cantly altered, as the attention of its leadership shifted back primarily 

to Indonesia rather than the Malay-Muslim Southeast Asia region as a whole. Key 

Jemaah Islamiyah operatives remained in Malaysia and the Philippines, however, and 

remained active there for a period. Hence, the portrait drawn from arrested operatives 

and captured documents was not entirely obsolete.

A document produced by the Jemaah Islamiyah leadership in Malaysia in May 

1996 — Pedoman Umum Perjuangan al-Jamaah al-Islamiyah [General Guideline 

for the Jemaah Islamiyah Struggle], or PUPJI, as Indonesian authorities came to call 

it — served as a virtual constitution, or by-laws, of the organization.228 Written in 

Arabic, one of the fi rst things a reader notes is that the document makes no mention of 

Indonesia or Southeast Asia, or any other country. Rather, it is conceptualized wholly 

in Islamic terms and probably bears close resemblance to parallel al-Qa'ida and later 

Taliban documents in Afghanistan. Arguing as a fi rst principle that the establishment 

of religion requires the establishment of an Islamic state, it begins by outlining the 

goal of Jemaah Islamiyah, which it sketches in seven stages:229

Formation and development of a Jemaah Islamiyah (which within the document 

it more clearly defi nes as a jemaah min al-Muslimin — a jemaah within the 

larger Islamic world)

Developing the strength of Jemaah Islamiyah

Using the strength of the Jemaah Islamiyah (through dakwah and jihad)

Establishing the Islamic State

Organizing the Islamic State

Strengthening the Islamic State

Coordinating and collaborating with other Islamic states to reestablish the 

Caliphate

227 Zachary Abuza, Militant Islam in Southeast Asia: Crucible of Terror (Boulder, CO: Lynn Reinner 

Publishers, 2003), 157. For details on the Singapore cell, 138 – 140.

228 The PUPJI document was fi rst discovered on the computer of Jemaah Islamiyah operative Imam 

Samudra, a key organizer of the October 12, 2002, bombing in Bali, Indonesia, who was arrested by 

Indonesian authorities on November 21, 2002. Translated into English by Dr. Rohan Gunaratna of the 

Singapore-based Institute for Defence and Strategic Studies, the document came into the author’s hands 

from a source that asked to remain anonymous. A copy of Dr. Gunaratna’s initial analysis of the document 

was provided with it. A search by the author suggests that the PUPJI document has not yet been posted on 

the Internet.

229 PUPJI, 4 – 5. 

1.

2.

3.

4.

5.

6.

7.
105

Presumably the fi rst Islamic state envisioned by the PUPJI need not be a regional 

one encompassing all the Malay Muslims of Southeast Asia nor even the whole of 

Indonesia. It might be a series of states within the region where Islamic sentiment was 

strong, such as Patani in southern Thailand, Kelantan and/or Terengganu in northern 

Malaysia, the Muslim islands of the southern Philippines, Aceh in northwestern 

Sumatra, and/or southern Sulawesi in eastern Indonesia. Once these were established 

as Islamic states, each would work to strengthen itself and collaborate with the 

others under the overall supervision of the amir of Jemaah Islamiyah to encourage 

the emergence of similar Islamic states, ultimately culminating in the emergence of 

a unifi ed Islamic state in southeast Asia that would in the longer run submerge itself 

under the authority of a reestablished Caliph of the entire Islamic world.

Return to Southeast Asia

Training as a means of developing a strong organization is given central emphasis 

in the document, and such training was the primary task of the new organization 

during its formative years in the late 1990s. Although Abd al-Rasul Sayyaf’s Camp 

Sadah in western Pakistan, and after 1992 his new camp at Torkham, was the major 

source of this training, the training effort was increasingly organized within the region 

as trained individuals returned. The full scope of this effort is not fully known. At 

least one Jemaah Islamiyah training camp was established in Malaysia itself, at Negri 

Sembilan.230 Other training centers were established in southern Thailand as well.231

By far the largest training effort was centered in the southern Philippines, however. 

By agreement with the Moro Islamic Liberation Front (MILF) in Mindanao, a Jemaah 

Islamiyah training camp, Camp Hudaibiyah, was opened up beginning in October 

1994 in a remote section of the MILF’s large Camp Abu Bakar.232 At the beginning, alQa'ida leader Abu Zubayda sent several Arabs, including Kuwaiti Omar al-Farouk233

and Algerian al-Mughira al-Gaza’iri, the commander of Camp Khaldun in Afghanistan, 

to oversee this effort.234 The role of Arab and other foreign al-Qa'ida trainers was a 

temporary one, however, as mainly Indonesian instructors soon took over most of this 

training. Some MILF personnel are also reported to have served as both instructors 

and trainees at Camp Hudaibiyah.

The arrangement lasted until July 2000, when Philippine Army forces took over 

Camp Abu Bakar, and then Camp Hudaibiyah in 2001. By this time, with the fall of the 

Suharto government in May 1998, Indonesian members of Jemaah Islamiyah began 

to return home, and various training camps began to be established there, especially in 

the eastern Indonesian islands, the Malukus and Sulawesi in particular. Collaboration 

between Jemaah Islamiyah and the MILF reportedly continued, however, with some 

230 See Chapter 2, 48. 

231 See Chapter 3, 73. 

232 See Chapter 6, 209. Also ICG. Damaged but Still Dangerous, 16 – 17. 

233 The Government of Kuwait has denied he is a Kuwaiti national.

234 Abuza, Militant Islam in Southeast Asia, 137.
106

MILF fi ghters receiving training in the new Indonesian Jemaah Islamiyah camps, and 

some Indonesians continuing to be seen in MILF areas of Mindanao.235

Secrecy of Jemaah Islamiyah

The need to maintain secrecy and discipline are two other themes that pervade the 

PUPJI document. Jemaah Islamiyah is conceptualized as an elite military organization, 

each of whose members has been carefully vetted during his recruitment process in 

accordance with these two criteria as well as for his “solid base” (al-qa'ida al-shulabah) 

in religion. Each is required to give an oath of allegiance (bai’a) to the `amir (Abdullah 

Sungkar), to listen carefully to the `amir’s instructions, and to obey them unwaveringly 

to the best of his abilities. The ability and desire to work together collectively, as well 

as to be mutually protective of other members of the group, are other key criteria for 

membership. At least a portion of the organization is defi ned as Tanzim Sirri (secret 

organization). The document is not clear whether this means all or a portion of Jemaah 

Islamiyah. Until the uncovering of the organization in December 2001, it succeeded in 

maintaining its clandestine nature, including its fi rst terrorist operations in 2000 (e.g., 

the Christmas Eve church bombings in Indonesia in December 2000) that occurred 

without attribution. Both of the known planned operations, the 1995 OPLAN Bojinka 

in the Philippines and the probable 2002 planned operations against U.S. facilities in 

Singapore, were meant to have been carried out by al-Qa'ida personnel with Jemaah 

Islamiyah support.236 They were not to have compromised the clandestine character of 

the organization until it had garnered the strength to be able to reveal its existence. 

Structure of Jemaah Islamiyah

The remainder of the PUPJI document is organizational in nature. At the head of 

Jemaah Islamiyah was the `amir (Abdullah Sungkar), said to have been chosen by 

the seven-man Syuro (shura) Council appointed by himself. Sungkar is alleged to 

have given bai`a to al-Qa'ida leader Usama bin Ladin,237 but this was not the basis 

of his authority in Jemaah Islamiyah. The `amir, in turn, was to be supported by four 

councils:

The Qiyadah (Leadership) Council, consisting of the leadership of three other 

councils:

 a. The Qiyadah Markaziyah (Central Leadership) Council

 b. The Qiyadah Mantiqiyah (Territorial Leadership) Council

 c. The Qiyadah Wakalah (Representative Leadership) Council

The Syuro (Consultative) Council (seven members)

The Fetwa (Legal Advice) Council

The Hisbah (Internal Judiciary) Council

235 International Crisis Group, Damaged but Still Dangerous, 23.

236 Abuza, Militant Islam in Southeast Asia, 139.

237 Abuza, Militant Islam in Southeast Asia, 127.

1.

2.

3.

4.
107

Not all of this structure may have been brought into being before the uncovering of 

Jemaah Islamiyah. Article 43, the fi nal article of the PUPJI, states, “This Constitution 

will be implemented in stages depending on available conditions.” One element that 

was established was the Qiyadah Council, which consisted of four mantiqi councils 

and a number of wakalah councils. The four mantiqi councils had purview over four 

territorial regions into which Southeast Asia was divided:

Mantiqi 1: Covered southern Thailand, the Malay peninsula, and Singapore. 

Headed by al-Qa'ida-trained (1987-1989) Indonesian, Riduan Isamuddin, 

better known as Hambali, until early 2002, when he was reportedly replaced 

by Ali Gufron (Muklas),238 this region was less a theater of operations than 

a headquarters organization engaged primarily in fundraising, planning, and 

logistical support for training in Afghanistan and later the southern Philippines. 

It was Hambali and others that established business operations in Malaysia that 

provided logistical support for al-Qa'ida operative Ramzi Yousef’s OPLAN 

Bojinka in late 1994-early 1995.

Mantiqi 2: Covered the main islands of Java, Sumatra, and Maluku in 

Indonesia, except for Sulawesi and Kalimantan. Headed by Mindanao-trained 

Abdullah Anshori, also known as Abu Fatih, region was considered the primary 

operational region of Jemaah Islamiyah.

Mantiqi 3: Covered the southern Philippines and all of Borneo, including 

Kalimantan (Indonesia), Sabah and Sarawak (Malaysia), and Brunei and 

Sulawesi (Indonesia). Headed by Pranato Yudha, more commonly called 

Mustopa, and also known as Abu Thalout, until his arrest in July 2003, this 

mantiqi was formed in 1997 as a means of more effectively administering 

the logistical requirements of Jemaah Islamiyah recruits receiving training 

at Camp Hudaibiyah in the southern Philippines. In military terms, it was a 

training command rather than an operations command.

Mantiqi 4: Covered cells in Australia and Papua (formerly Irian Jaya), although 

not Papua New Guinea. Headed by an unidentifi ed individual called Abdul 

Rohim, this mantiqi was formed sometime before December 2001, primarily 

for the purpose of fundraising and recruiting Indonesian and other southeast 

Asian Muslims residing in these areas for Jemaah Islamiyah training, providing 

organizational structure, and possibly future operational planning.

Each of these regions was further subdivided into wakalah, which in turn were 

further divided into khatibah, qirdas, and fi ah. Although these were territorial divisions, 

the terms also refl ected the hierarchical military structure of Jemaah Islamiyah into: 

mantiqi (brigades), wakalah (battalions), khatibah (companies), qirdas (platoons), 

and fi ah (squads).239 A number of walalah were established. Those so far known 

include, in Malaysia: Kuala Lumpur/Selangor, Johor, Kuantan, Perak, Kelantan, and 

238 International Crisis Group, Damaged but Still Dangerous, 11. Gufron was headmaster of Pondok/

Pesantren Luqmanul Hakiem, which he helped Sungkar and Ba’asyir establish in Johor in 1991.

239 International Crisis Group, Damaged but Still Dangerous, 11.

1.

2.

3.

4.
108

Negri Sembilan; the wakalah of Singapore240; Wakalah Hudaibiyah in the southern 

Philippines241; and in Indonesia: Jakarta, Medan, Pakanbaru, Lampung, Solo, 

Surabaya, Nenado, Makassar, Poso/Palu, East Kalimantan, and Nosa Tengara.242

During Jemaah Islamiyah’s period of development in the late 1990s, each of these 

divisions was focused primarily on recruitment and training, developing effective 

communications throughout the hierarchy, collecting information, and presumably 

planning. Aside from supporting OPLAN Bojinka in 1994 – 95, no operational 

(terrorist) activity is known to have occurred243 until the year 2000. By this time, 

however, a new era had dawned with the May 1998 fall of the Suharto regime in 

Indonesia, and the whole perspective of the Jemaah Islamiyah leadership changed 

from one of preparation into one of action.

FALL OF THE SUHARTO REGIME

As throughout the rest of Southeast Asia, the sudden devaluation of Thai currency in 

July 1997 produced a fi nancial crisis that soon reached Indonesia as well. Immediately, 

the value of the Indonesian rupiah began to fall. By August, when it had declined by 

nine percent, the government abandoned further efforts to sustain its value by injecting 

cash into the economy. As the rupiah went into freefall, reaching RP 4,000 to U.S. 

$1.00 in October, RP 5,000 to U.S. $1.00 in December, and RP 17,000 to U.S. $1.00 by 

January 1998, interest rates soared.244 Foreign capital, which for so long had fueled the 

Indonesian economy at an annual growth rate of nearly eight percent for nearly three 

decades, now suddenly began to fl ee the country, and “so too did billions of dollars 

of local capital.”245 Infl ation became rampant, debt-ridden businesses and banks 

collapsed, and nearly 14 million Indonesians had been made unemployed during the 

fi rst eleven months of the crisis246 that, in the case of Indonesia, has not been overcome 

even today.

Efforts of the International Monetary Fund (IMF) to restore confi dence in the 

rupiah (with a U.S. $38 billion loan package) also fl oundered, due in part to political 

240 Reported on in detail in Republic of Singapore, White Paper: The Jemaah Islamiyah Arrests 

and the Threat of Terrorism (Singapore: Ministry of Home Affairs, January 7, 2003). URL: http://www.

channelnewsasia.com/cna/arrests/whitepaper.pdf. Accessed October 22, 2005.

241 International Crisis Group, Southern Philippines Backgrounder, 16. The initial head of this wakalah 

was Fathur Rahman al-Ghozi.

242 International Crisis Group, Damaged but Still Dangerous, 12.

243 The assumption here is that terrorist activities of the Abu Sayyaf Group (ASG) in Basilan, Mindanao, 

and Sulu in the southern Philippines during this period were independent of Jemaah Islamiyah involvement. 

Although clear linkages existed between al-Qa'ida and the ASG, there is little evidence of connection 

between Jemaah Islamiyah and the ASG aside from a limited degree of joint training in MILF camps in 

Mindanao.

244 Judith Bird, “Indonesia in 1997: The Tinderbox Year,” Asian Survey, 38, 2 (February 1998), 173.

245 Greg Barton, “Islam and Politics in the New Indonesia,” in Islam in Asia: Changing Politcal Realities, 

ed. by Jason F. Isaacson and Colin Rubenstein (New Brunswick, NJ: Transaction Publishers, 2002), 14.

246 Ressa, Seeds of Terror, 54.
109

uncertainty about Suharto’s age (70) and health, but also because of the President’s 

evident reluctance to implement the package of economic reforms imposed upon him 

by the IMF.247 The crisis also exposed the well-known but heretofore impossible-topublicly-discuss cronyism and corruption of the ruling regime. Particularly involved 

were members of Suharto’s immediate family and a number of wealthy Chinese 

businessmen whose economic stakes in the country could be seriously undermined by 

strict compliance with the IMF-mandated reforms. As long as the Indonesian economy 

had remained strong, and investments could be made in improved health services as 

well as in providing educational and employment opportunities, the Army-dominated 

Suharto regime was able to maintain its fi rm and sometimes brutal stranglehold on 

Indonesia’s political life. Opposition had remained marginalized and had been forcibly 

suppressed whenever it appeared threatening. With the sudden transformation of 

Indonesia from a “miracle” economy into a “melt-down” economy dependent on 

the charity of the international aid community and donor countries for its continued 

survival, opposition to Suharto’s continued rule grew rapidly and became general. Put 

in traditional Indonesian terms, the Sultan appeared to have lost his wayhu, the ability 

to create order in the universe.248

Broad societal opposition to Suharto coalesced following his announcement 

on January 20, 1998, that he intended to run again for his seventh fi ve-year term as 

President of Indonesia, when the Parliament convened in March.249 Although he had 

governed with dictatorial authority since assuming power in 1965, Suharto had never 

abandoned the appearance of a republican form of government, nor a capitalist image 

of the Indonesian economy, although most of it was state-owned and operated by the 

military. Instead, he had driven all political activity into three political parties, one 

of which was his own government-based Golkar Party. Requiring all political offi ceseekers to be approved by his government as a condition for running for offi ce, he 

then relied on police-state tactics to ensure a signifi cantly large enough vote (usually 

65 – 70 percent) for Golkar. In such a manner, the May 1997 parliamentary elections 

had proceeded, and Suharto once again in March 1998 found himself unanimously 

reelected President of the Republic, despite abundant evidence of massive opposition 

to his continued rule throughout the country.

With the mandate of a new election behind him, Suharto began to implement the 

more than 100 IMF economic policy reforms required of him to stabilize the Indonesian 

economy. Among these was the abolition or reduction of government subsidies for a 

variety of basic commodities. One, announced on May 4, was a fuel subsidy reduction 

that meant a 70 percent increase in gasoline prices. Anti-government demonstrations 

had already emerged on university campuses, but spread across the country with 

247 Howard Dick, “Brief Refl ections on Indonesia’s Economic History,” in Indonesia Today: Challenges 

of History, ed. by Grayson Lloyd and Shannon Smith (New York: Rowman and Littlefi eld Publishers, 

2001), 164.

248 Ressa, Seeds of Terror, 55.

249 Indonesian Presidents are chosen by the Parliament. The last parliamentary elections had been held in 

May 1997, just before the outbreak of the Asian fi nancial crisis. Bird, “Indonesia in 1997,” 60.
110

this announcement. No violence had yet erupted, but did so after May 12 when four 

students from the prestigious, upper-middle class Catholic Trisakti University were 

shot dead by snipers, believed to be loyal to Suharto’s son-in-law, Lieutenant General 

Prabowo, while returning to their campus from a peaceful demonstration.250 Ten days 

later, Suharto was gone.

What followed was an upheaval in Jakarta that saw days of savage rioting in the 

Chinese and commercial sections, including an undetermined number of rapes of 

Sino-Indonesia girls and women; a death toll from mob violence that mounted to over 

a thousand souls; and an orgy of looting, plundering, and torching of malls and the 

houses of ethnic Chinese. By May 14, foreign embassies were evacuating personnel 

and President Soeharto was winging his way back from the G-15 summit in Cairo. The 

military-after some bizarre absences from the districts of confl ict-seemed to regain 

control of the situation the next day. The students massed and marched to Parliament, 

vowing to oust Soeharto, and the elite began to turn against him. On the 19th, Soeharto 

spoke on national television, vowing to leave offi ce in due time after new elections 

and the setting up of a reform committee in a phased process. But again it was too 

late. By that evening he discovered that the Muslim hierarchy wanted him to go, with 

ABRI chief General Wiranto saying he would protect Soeharto if he stepped down. 

Harmoko, Soeharto’s most trusted fl ack and head of the ruling GOLKAR organization, 

said the party and Parliament wanted him out, and most of his cabinet resigned. The 

grand chessmaster who had ruled for 32 years had been checkmated. On the morning 

of May 21, Soeharto resigned in a simple ceremony while a hesitant and tense Vice 

President Habibie took the oath of offi ce, followed by a short declaration from Wiranto 

of ABRI’s fealty to the Constitution and the new President.251

The collapse of the Suharto regime left the country in a long period of political 

turmoil characterized by a gravely weakened central government. The widespread 

popular upheaval of 1998 appeared to signify a societal rejection of the tradition of 

authoritarian rule that had long characterized Indonesia-fi rst under the Dutch and then 

under both Sukarno and Suharto. The need for reformasi that served as the battle cry 

of the demonstrators demanding an end to the Suharto regime refl ected a widespread 

vision of the early years of the new Indonesian republic before 1957 as a “golden age,” 

when democratic institutions, however anarchic, had fl ourished.252 As it turned out, 

the Constitution and its republican institutions have thus far prevailed, although at the 

cost of considerable political turmoil.

250 Barton, “Islam and Politics,” 15.

251 Judith Bird, “Indonesia in 1998: The Pot Boils Over,” Asian Survey, 39, 1 (January/February 1999), 

29.

252 Jean Gelman Taylor, Indonesia: Peoples and History (New Haven, CT: Yale University Press, 2003), 

339.
111

After Suharto

B.J. Habibie, who replaced Suharto as President, had been chosen as the latter’s 

Vice President in January 1998, many asserted, because Suharto had judged that 

few in the Indonesian political spectrum would want Habibie to replace him.253 A 

diminutive, eccentric fi gure, with peculiar mannerisms that led many to consider him 

a man lacking presidential stature,254 Habibie nevertheless had been patronized by 

Suharto since his youth, and in turn was one of the former President’s staunchest allies. 

A West German-trained aeronautical engineer, he had returned to Indonesia in the 

1970s to become director of the state-controlled aircraft industry, prior to being made 

Minister of Research and Technology, in charge of Indonesia’s “strategic industries,” 

which included the manufacture and procurement of armaments for the Indonesian 

Armed Forces.255 Known primarily for his overriding passion for the manufacturing 

of aircraft, he nevertheless was picked by Suharto in 1990 to serve as the director of 

the newly established Association of Muslim Intellectuals (ICMI).256 Not particularly 

known for his religious piety, Habibie nevertheless was a close associate of the 

President, and his appointment as director of ICMI communicated the importance 

Suharto attributed to the new institution. The symbolism of associating Islam with 

modern science, technology and industrial development was yet another factor behind 

the choice of Habibie.

CNN corespondent Maria Ressa suggests that historians will be kinder to Habibie 

than his contemporaries were “to this enthusiastic man with boundless energy, who 

accomplished more in his sixteen months in offi ce than anyone could have expectedpassing more than twelve hundred laws, releasing political prisoners, and strengthening 

political institutions.”257 Unable to maintain the confi dence of the Parliament, however, 

Habibie agreed to authorize new national elections in June 1999, although there was no 

Constitutional requirement for him to do so. The elections, held on June 7, 1999, were 

the fi rst free and fair elections conducted in Indonesia since 1955. Habibie himself had 

removed the ban on political parties (besides the three the Suharto government had 

sanctioned), and more than 140 had formally registered with the government by the 

end of 1998. Of these, 46 were judged by the Interior Ministry as having the minimum 

requirements to be included on the ballot, and 21 of these parties gained seats in the 

new Parliament elected in June 1999.258

253 Bird, “Indonesia in 1998,” 28.

254 Ressa, Seeds of Terror, 55.

255 Greg Barton, “Assessing the Threat of Radical Islamism in Indonesia,” 15, fn. 26. Draft paper 

published on the Internet. URL: http://www.sisr.net/apo/Islamism_in_Indonesia.rtf. Accessed April 15, 

2005.

256 See above, 91.

257 Ressa, Seeds of Terror, 55.

258 Greg Fealy, “Parties and Parliaments: Serving Whose Interests?” in Indonesia Today: Challenges 

of History, ed. by Grayson Lloyd and Shannon Smith (Lanham, MD: Rowman and Littlefi eld Publishers, 

2001), 100.
112

Table 6.1

The 1999 General Election Results and Parliamentary Seats for Major Parties

Party Votes %

No. of 

Seats

1 PDI-P (Indonesian Democratic Party of Struggle) 33.76 153

2 Golkar (Functional Groups Party) 22.46 120

3 PKB (National Awakening Party) 12.62 51

4 PPP (United Development Party) 10.62 58

5 PAN (National Mandate Party) 7.12 34

6 PBB (Crescent Moon and Star Party) 1.94 13

7 PK (Justice Party) 1.36 7

8 PKP (Justice and Unity Party) 1.01 4

9 PNU (Muslim Community Awakening Party) 0.64 5

10 PDKB (Love the Nation Democratic Party) 0.52 5

Eleven other parties 7.85 15

Source: Greg Fealy, “Parties and Parliaments: Serving Whose Interests?” in Indonesia Today: 

Challenges of History, ed. by Grayson Lloyd and Shannon Smith (Lanham, MD: Rowman and 

Littlefi eld Publishers, 2001), 101.

Generally considered by international observers to have been “free and fair” 

elections, the outcome was believed to be reasonably refl ective of the complex political 

landscape that Indonesia constituted. Five parties gained 85 percent of the votes. The 

major winner was the PDI-P, headed by the daughter of former President Sukarno, 

Mrs. Megawati Sukarnoputri. Observers noted that, despite the increased santrifi cation

(Islamization) that had characterized Indonesian society over the last two decades, the 

combined Islamic parties favoring a shari`a-based state — as opposed to one based on 

Pancasila — gained only 18 percent of the vote, signifi cantly less than the approximately 

40 percent a parallel grouping had won in the 1955 elections.259 Nevertheless, partly 

because of a lingering bias against choosing a woman as President, Megawati was 

unable to muster suffi cient support among the members of the Parliament to win the 

election.260 Instead, after a complex political process, the choice fell upon third-place 

PKB leader Abdurrahman Wahid. Megawati was in turn elected as Vice President, and 

both were installed in offi ce, replacing Habibie, on October 20, 1999.

259 Theodore Friend, Indonesian Destinies (Cambridge, MA: The Belknap Press of Harvard University 

Press, 2003), 391. It should be noted that Muhammadiyah had accepted Pancasila, when required to do so 

in 1984, and its 1999 political manifestation, PAN, under the leadership of Amien Rais, continued to do so 

as a matter of principle. Friend, Indonesian Destinies, 389.

260 Friend, Indonesian Destinies, 392.
113

Presidency of Gus Dur

The grandson of two founders of the 40 million-strong, abhangen-based mass 

organization, Nahdlatul Ulama, Wahid (or Gus Dur, as he was more popularly 

known) had assumed leadership of the Nahdlatul Ulama in 1984. Although deeply 

rooted in Indonesia’s rural-based, syncretic abhangen Islamic religious tradition, 

Wahid was also a liberal modernist, closely associated with the “neo-modernist” 

school of Nurcholish Madjid that President Suharto had empowered through the 

creation of the ICMI in 1990.

An enigmatic figure whose strengths (articulate idealism combined with 

bewildering tactical maneuvering) as an opposition figure became weaknesses in 

the office of the Presidency, Wahid also had the misfortunate to have suffered a 

stroke in January 1998. Although he made a reasonably good recovery, the stroke 

greatly reduced his stamina and also caused him to become legally blind.261 His 

“middle way” approach to handling the country’s manifold political, economic, 

and social problems failed to satisfy more radical elements on both sides of 

Indonesia’s political spectrum, particularly the Army whose support he could 

never gain.262 His key dilemma was how to serve as a strong President when 

he himself, as well as a majority in the Parliament that had elected him, wanted 

to curtail the powers of the Presidency in the interests of a stronger democracy. 

Without a sufficiently strong political base within the Parliament, and increasingly 

perceived as lacking the leadership qualities needed to guide the country, he was 

impeached by the Parliament in a unanimous 591 to 0 vote in July 2001. His Vice 

President, Megawati Sukarnoputri, took over as President for the remainer of 

his five-year term. Hamza Haz, leader of the Suharto-era Islamic party, the PPP, 

and one of Wahid’s fiercest critics, as well as of Megawati, was chosen as the 

replacement Vice President.263

Megawati, Indonesia, and September 11, 2001

Long a fi rm opponent of Suharto, in part because of his “non-person” treatment 

of her father, Megawati too had suffered the brutality of the former President’s 

regime, when in July 1996, fully a year before the scheduled national elections of May 

1997, government forces had attacked the headquarters of her increasingly popular 

261 Barton, “Islam and Politics in the New Indonesia,” 29.

262 For capsule views of Wahid’s personality and character, see John L. Esposito and John Voll, Makers 

of Contemporary Islam (New York: Oxford University Press, 2001), Chapter 9, “Abdurrahman Wahid,” 

199 – 216. Also Greg Barton, “Indonesia’s Nurcholish Madjid and Abdurrahman Wahid as Intellectual 

Ulama: The Meeting of Islamic Traditionalism and Modernism in Neo-Modern Thought,” Islam and 

Christian-Muslim Relations, 8, 3 (October 1997), 323 – 350. Also Barton, “Islam and Politics in the New 

Indonesia,” 76 – 84.

263 Michael S. Malley, “Indonesia in 2001: Restoring Stability in Jakarta,” Asian Survey, 41, 1 

(January – February 2002), 124.
114

PDI-P political party, resulting in a number of deaths.264 Megawati’s strength was 

that she was the bearer of her father’s legacy that was increasingly being perceived 

nostalgically during the latter years of the Suharto era. Otherwise, she did not prove to 

be an effective politician, as was demonstrated by her failure to be elected President, 

despite her party’s victory in the 1999 elections. Now made President almost by 

default following the July 2001 impeachment of Abdurrahman Wahid, she owed much 

politically to the Islamic parties in the Parliament that had turned against Wahid. 

This was particularly true of PPP leader Hamza Haz, the virtual “kingmaker” of her 

Presidency who now served as her Vice President. No longer bound by Suharto’s 1984 

“sole ideological principle” requiring all organizations, including political parties, to 

support Pancasila as the “civil religion” of the state, the contest between those, like 

Megawati and the PDI-P, who continued to champion Pancasila, and those like Haz 

and the PPP, who favored replacement of Pancasila by the shari`a, resumed. Although 

the 1999 elections suggested overwhelming public support for Pancasila, the political 

dependence of Megawati on the support of the Islamic parties made the contest a more 

even one than the 1999 elections implied.

The United States’ response to the September 11, 2001, attacks on the World Trade 

Center and the Pentagon at fi rst appeared to strengthen Megawati’s hand politically. 

The December 2001 Singapore discovery of Jemaah Islamiyah, its linkages to the 

al-Qa'ida sponsors of the September 11 attacks on the United States, and knowledge 

that the Jemaah Islamiyah leaders had returned to Indonesia in early 1999 following 

the collapse of the Suharto regime, placed a spotlight on Indonesia in U.S. President 

George W. Bush’s global war on terrorism. Whereas U.S.-Indonesian relations had 

been very strained since the Indonesian Army-supported militia violence in East 

Timor following the August 30, 1999, UN-sponsored referendum on East Timorese 

independence (79.5 percent in favor), the United States now sought improved 

relations with the Megawati government and support for the war against terrorism. 

Although Megawati was keen to restore good relations with the United States, she 

was constrained by the Islamic parties who feared that the war against terrorism 

could in fact become a war on Islam, particularly in Indonesia.265

Accordingly, despite lip-service support for U.S. opposition to terrorism,266

until the October 2002 Jemaah Islamiyah-sponsored bombing of the Sari nightclub 

in Denpasar, Bali, Indonesian authorities tended to deny the existence of any 

signifi cant terrorist threat in Indonesia-this despite several pre-9/11 terrorist attacks 

on Indonesian soil. These included the attempted assassination of the Philippine 

264 Ressa, Seeds of Terror, 52 – 53. The aim of the attack was to “encourage” the party to choose someone 

other than Megawati as its leader. The effort failed and probably only strengthened the party’s and her 

appeal among the Indonesian public.

265 Ann Marie Murphy, “Indonesia and the World,” in Indonesia: The Great Transition, ed. by John 

Bresnan (Lanham, MD: Rowman and Littlefi eld Publishers, 2005), 271.

266 Offi cially, Megawati, refl ecting widespread popular opinion in Indonesia, expressed grave reservations 

about U.S. military operations in Afghanistan, stating that “international regulations and conventions should 

be followed to ensure that the war on terrorism did not become a new form of terrorism itself.” Murphy, 

“Indonesia and the World,” 276.
115

Local police post in Bali in 2000. This was the site of the Jemaah Islamiyah-sponsored 

bombing of a nightclub in October 2002, which killed scores of tourists.

Source: 

Table 6.2

The 2004 General Election Results

Party Votes %

Golkar (Functional Groups Party) 21.6

PDI-P (Indonesian Democratic Party for Struggle) 18.5

PKB (National Awakening Party) 10.6

PPP (United Development Party) 8.2

PD (Democratic Party) 7.5

PKS (Prosperous Justice Party) 7.2

PAN (National Mandate Party) 6.4

PBB (Crescent Moon and Star Party) 2.6

Other parties 17.3

Source: R. William Liddle and Saiful Mujani, “Indonesia in 2004: The Rise of Susilo Bambang 

Yudhoyono’’ in Asian Survey, 45, 1 (January/February 2004), 120.
116

Ambassador to Indonesia in Jakarta (August 2000); the bombing of the Jakarta 

Stock Exchange (August 2000); the Christmas eve bombing of 30 churches 

throughout Indonesia (December 2000); and the bombing of the Atrium Shopping 

Center in Jakarta (August 2001). The later March 2003 U.S. invasion of Iraq totally 

undercut her relationship with the United States, however, as popular support for 

U.S. President Bush sank to a low of 15 percent in Indonesia.267

Although Megawati managed to remain in offi ce for the remainder of her 

constitutional term, her effort to be reelected in 2004 failed. Instead, former President 

Suharto’s offi cial party, Golkar, reemerged as the strongest party electorally, perhaps 

suggesting a degree of nostalgia for the more orderly Suharto years. For President, the 

electorate, now voting across the country for the fi rst time, chose a relatively unknown 

retired general, Susilo Bambang Yudhoyono, who previously had been coordinating 

minister for political and security affairs in Megawati’s cabinet. Yudhoyono had taken 

the precaution of forming his own political party (PD) in 2001 as a vehicle to support 

his Presidential candidacy. His overwhelming victory over Megawati should perhaps 

be seen more as a rejection of her rather than a positive affi rmation of Yudhoyono. 

Nevertheless, the process signaled the continued, successful operation of Indonesia’s 

restored constitutional democracy-the desire for which appears uppermost in the minds 

of most Indonesians in the post-Suharto era, despite the myriad problems that continue 

to beset the country during the reformasi period.

267 Murphy, “Indonesia and the World,” 176.
117

CHAPTER 5

SEPARATISM: THREAT TO INDONESIAN UNITY?

REVIVAL OF SEPARATISM IN INDONESIA

Problems facing the reformasi era included a failure of the Indonesian economy 

to rebound effectively following the 1997 Asian fi nancial crisis, but perhaps the most 

serious problem was the revival of long dormant separatist movements that threatened 

the unity of the Indonesian state. Among these were the confl icts that emerged in East 

Timor, the Maluku Islands, Sulawesi, Irian Jaya (Papua), Kalimantan, and Aceh, where 

elements of the native population took advantage of a weakened central government 

following the fall of Suharto to revive historic claims to independence. Except for 

Aceh, whose population is Muslim, and where the quest for independence is based on 

different foundations, each of the other areas is characterized by a signifi cant Christian 

population, so that struggles to achieve freedom from Indonesian rule tend to have 

the appearance of Christian-Muslim confl ict. It was primarily in these confl icts that 

Jemaah Islamiyah and other related militant Islamic groups found scope for action in 

the post-Suharto era.

Dutch policy during the colonial era generally forbade Christian missionaries 

from teaching or establishing schools or hospitals in Muslim communities. Rather 

they were directed to areas where the local population had not yet accepted Islam.268

These populations also were generally in the peripheral areas of the colonial state and 

consisted of different tribal groups so that what sometimes appeared as Christian/

Muslim religious confl ict was also, in fact, ethnic confl ict. Examples of largely 

Christian ethnic groups are the Dyacks of Kalimantan, the Minahasa of northern 

Sulawesi, the Ambonese of Ambon (Maluku), and the Irianese of Papua. As Christians, 

these groups typically received favorable treatment by the Dutch authorities.269 The 

Ambonese, for example, served as the backbone of Dutch police and security forces 

throughout the archipelago. As a result, when the Dutch sought to reestablish their 

rule after World War II, these groups generally fought alongside the Dutch against the 

Indonesian nationalists and favored a continuation of Dutch rule and/or recognition 

as independent Christian states. For this reason, a group of Christian Ambonese 

declared the birth of the independent Republic of the South Moluccas in 1950.270

The separatist movements were rapidly crushed by the new Indonesian Republic, 

however, that was determined to lay claim to all the lands that had been brought under 

control by the Dutch. Successfully suppressed by the young Indonesian Republic, they 

remained dormant until an opportune time, when a weakened central government that 

followed the end of the Suharto regime in 1998 opened the door to renewed separatist 

tendencies.

268 Taylor, Indonesia, 259.

269 Taylor, Indonesia, 268 – 270.

270 Taylor, Indonesia, 342.
118

EAST TIMOR

East Timor was a special case. Never part of the Dutch East Indies (as was West 

Timor), it had remained, like East Papua (formerly a colony of Australia; today Papua 

New Guinea), a colonial possession of Portugal. With Portuguese rule came Christianity. 

When Portugal made its decision to withdraw from East Timor (in 1975), although 

only 30 percent of the native population was Christian, these constituted the “ruling 

elite” of the half-island that was both Portuguese-speaking and Roman Catholic.271

Among this elite, three parties emerged to compete with one another for control of postcolonial East Timor. The Timorese Democratic Union preferred union with Portugal 

and wanted Portuguese to remain the offi cial language of administration. Fretilin also 

wanted Portuguese to be the offi cial language of East Timor, but favored independence 

in a commonwealth relationship with Portugal. The Timorese Popular Democratic 

271 Taylor, Indonesia, 379. The remaining 70 percent were animist in religion, venerating local spirits of 

the land and the sky. There were virtually no Muslims among the indigenous Timorese population.

Map of East Timor, long claimed by Indonesia and now a UN protectorate.

Source: CIA.
119

Association, on the other hand, favored union with West Timor, incorporation into 

Indonesia, and the adoption of Bahasa Indonesia as the offi cial language.272

This last party had the support of the government of Indonesia, whose President 

Suharto viewed incorporation of East Timor into Indonesia as the only acceptable 

option. Accordingly, it provided arms, military training, and funds to pro-Indonesian 

forces that provoked clashes with pro-independence forces, especially Fretilin, which 

nevertheless succeeded in taking control of East Timorese government institutions as 

the last Portuguese troops departed the island in August 1975. Undeterred, the Suharto 

government succeeded in portraying Fretilin as a communist-inspired movement that in 

the wake of the fall of Vietnam, Cambodia, and Laos to communist forces in this period 

threatened yet further expansion of communism in Southeast Asia. Accordingly, the 

Western powers, particularly the United States and Australia, acquiesced in Suharto’s 

decision to invade East Timor in December 1975 and to annex it the following year 

as Indonesia’s 27th province.273 The United Nations, however, never recognized 

Indonesian sovereignty over East Timor and continued annually until 1982 to call for 

a “self-determination” referendum to decide the political fate of East Timor.274

Although Fretilin was defeated, its forces retreated to the rugged mountainous 

interior and continued to wage guerrilla warfare against Indonesia’s “occupation 

forces.” Indonesian counterinsurgency efforts proved especially brutal, as most native 

Timorese were eventually uprooted and moved into designated “strategic hamlets” that 

usually were ill-suited for agricultural production. Estimates of 100,000 to 200,000 

deaths among a pre-war population of 650,000 highlighted the brutality of Indonesian 

rule and kept the East Timor question alive at the international level.275

Indonesian Rule in East Timor 

Another Suharto strategy common to all the “Christian” areas of Indonesia 

that were seen as areas of potential separatist sentiment was to encourage internal 

Muslim transmigration. In East Timor, use of the Portuguese language was banned, 

and only Bahasa Indonesia could be used in government offi ces, schools, and public 

business. Only the Indonesian state school curriculum could be taught in schools, and 

appointed government positions were restricted to Indonesian speakers who possessed 

certifi cates denoting offi cial Pancasila training. In due time, the former Portuguesespeaking Roman Catholic elite had been replaced by an Indonesian-speaking Muslim 

272 Taylor, Indonesia, 380.

273 Virtual Information Center, East Timor Primer, updated 29 November 2004, 7 – 8. URL: http://www.

vic-info.org/RegionsTop.nsf/0/140323653b451c978a256aabb0002a3dc?OpenDocument. Accessed April 4, 

2005.

274 Murphy, “Indonesia and the World,” 253.

275 Murphy, “Indonesia and the World,” 253.
120

elite, mostly immigrants from elsewhere in the country who increasingly controlled 

the economic as well as the political life of East Timor.276

The imposition of Indonesian rule, however, had a contrary consequence. In order 

to meet the state’s Pancasila requirement that all citizens subscribe to a monotheistic 

religion, the large majority, at least 80 – 85 percent, of East Timor’s animists chose to 

register as Roman Catholics, a development the Catholic Church, through its Indonesian 

priesthood, aggressively sought to consolidate.277 An impact of this change was 

that continuing government efforts to suppress the Fretilin-led insurgency was 

increasingly perceived internationally in religious terms, as Muslim persecution 

of Christians.

A particularly egregious event occurred in November 1991, when government 

troops pursued and fi red upon a Christian funeral procession in the East Timor capital 

of Dili, killing more than 200 and injuring many more. Later called the “Santa Cruz 

Massacre,” after the name of the cemetery toward which the mourners were marching, 

the incident was caught on fi lm by international journalists and smuggled out of the 

country. The deceased had been a well-known pro-independence activist, and during 

the procession banners had appeared calling for independence and celebrating the 

Fretilin guerilla leader Xanana.278 Government efforts to explain the episode as 

dealing with “an unacceptable infraction of public order” were belied, however, by 

the fi lm images of Indonesian troops fi ring on unarmed, fl eeing civilians, some trying 

unsuccessfully to save their lives by hiding behind gravestones.279

The Santa Cruz massacre brought the East Timor question back into the international 

spotlight. “The European Community condemned the event and within weeks the 

Dutch, Canadians and Danish governments had suspended aid programs to Indonesia. 

The facilitating role that U.S. weapons played in Indonesia’s actions received great 

publicity, and Congress responded in 1992 by severely restricting Indonesia’s access 

to American military education and training.”280 Leading the effort to publicize 

internationally the “hell” in which most East Timorese lived under Indonesian rule 

was Bishop Carlos Felipe Ximenes Belo of East Timor and Fretelin publicist (living 

in exile) Jose Ramos Horta, both of whom found themselves fêted for their courage by 

award of the Nobel Prize for Peace in 1996. Despite mounting international pressure to 

permit the long-demanded, UN-supervised referendum on self-determination in East 

Timor, Suharto remained fi rm in his determination to establish effective control of the 

“province.” In 1997 the Army labeled its counterinsurgency campaign in East Timor 

“Operation Eradicate,” and in 1998 “Operation Clean Sweep.”281

276 Taylor, Indonesia, 381.

277 Taylor, Indonesia, 381.

278 Later President of independent Timor Leste, José Alexeandre Gusmao.

279 Friend, Indonesian Destinies, 275 – 276.

280 Murphy, “Indonesia and the World,” 256.

281 Friend, Indonesian Destinies, 433 – 434.
121

A False Illusion 

The 1997 Asian fi nancial crisis and the consequent May 1998 collapse of the 

Suharto regime, however, posed many problems for Indonesia, including a grave 

weakening of central government authority. Under strong international pressure, 

successor President B.J. Hababie, “in a moment of inspiration” in January 1999, 

suddenly decided to relieve himself of the East Timor problem by agreeing to permit 

the UN-sponsored referendum. Arguing that the East Timorese would likely vote for 

autonomy under Indonesian sovereignty rather than independence, he sought to make 

the case domestically that such a referendum would resolve the East Timor question 

once and for all. In the unlikely event they did vote for independence, Indonesia would 

be rid of a problem that had drained its resources for far too long. In either case, 

the country would be better positioned to restore its relations with the international 

community that had become strained over the East Timor question. Privately, Habibie 

also seemed to believe that fi nal resolution of the East Timor problem would enhance 

his stature politically and help to strengthen the likelihood of his being reelected 

President later in the year. How wrong he was became clear at the time of the October 

presidential elections, when his East Timor policy emerged as the major complaint of 

those parliamentarians voting against him.282

In accordance with Habibie’s agreement, the fi rst elements of the UN’s International 

Force in East Timor (INTERFET) moved into its capital, Dili, on June 4, 1999, and the 

referendum took place on August 30. Despite efforts of the Army’s Eastern Division 

Command, under Major General Zacky Anwar Makaram, to sabotage the referendum 

and eliminate leaders of the independence movement, both before and after the vote, 

an astonishing 98.5 percent of registered voters participated in the referendum, and 

78.5 percent of them voted against autonomy, thereby beginning a process leading to 

independence for East Timor by the terms of the referendum.283

The overwhelming vote in favor of independence did not immediately ameliorate 

conditions in East Timor, however. Pro-Indonesian militia, acting in concert with 

army and police offi cials in the country, embarked on a reign of terror, burning 

towns and villages and displacing hundreds of thousands of East Timorese, forcing 

most to take refuge in West Timor. The continued efforts of hardline elements of the 

Indonesian armed forces and their East Timorese supporters to challenge the outcome 

of the referendum, despite the formal policy of the government, led the international 

community to force Indonesia to acquiesce in permitting a larger international force, 

the United Nations Transitional Administration for East Timor (UNTAET), to take 

charge of the administration of the country. This force took over from INTERFET in 

November 1999, enforced law and order, and administered East Timor until its transfer 

of sovereignty to an independent East Timor (Timor Leste) on May 20, 2002.

282 B. William Liddle, “Indonesia in 1999: Democracy Restored,” Asian Affairs, 40, 1 (January/February 

2000), 37.

283 Virtual Information Center, East Timor Primer, 9.
122

Despite the offi cial acquiescence of the Indonesian government to the loss of 

East Timor, the loss was perceived domestically as a national humiliation. That 

Timor was an integral part of Indonesia was the fi rm view of both the nationalist and 

Islamist wings of the Indonesian political spectrum. In the view of most, international 

determination to secure the independence of East Timor raised fears that the very 

unity of the Indonesian state was threatened. Similar movements in other parts of the 

country posed potential threats to this unity, or so many Indonesians believed.

Map of the group of Indonesian islands known as Maluku.

Source: CIA.
123

MALUKU AND LASKAR JIHAD

The Indonesian province of Maluku in the far east of the archipelago consists of 

approximately 1,000 islands scattered over about 1.5 million sq. km. of area that 

constitutes the province. Called by the early European explorers and traders the “Spice 

Islands” because of the cloves, nutmeg, and mace that at the time were grown only 

there and were much in demand in Europe and elsewhere, they nonetheless are remote 

from the central government authority in Jakarta. Moreover, the province’s relatively 

small population of two million constitutes less than one percent of Indonesia’s total 

population. Economically, particularly the northern islands of Maluku together with 

neighboring Sulawesi to the west, are as much in the trading orbit of the southern 

Philippines, just to the north, as they are to the main Indonesian island of Java that 

holds 50 percent of Indonesia’s population. Nevertheless, it was the Dutch rather than 

the Spanish who established monopoly control over trade with the Spice Islands, 

and Maluku was part of the Dutch empire that in 1950 was inherited by the newly 

established Indonesian government.

Culturally, Maluku also is highly diverse ethnically, inhabited by peoples speaking 

129 languages.284 Religiously, although Islam came fi rst to the islands, which were 

and remain the site of several sultanates (Ternate, Tidore, Banda), the sultans ruled 

an ethnically diverse population, most of whose non-Muslim inhabitants became 

Christians during the period of Dutch rule. Prior to the violence that erupted in 

Maluku in 1999, Christians constituted approximately 40 percent of the total Maluku 

population, whereas Muslims made up about 59 percent.285

During the Suharto years, a government policy of encouraging Muslim 

transmigration, particularly from overpopulated Java to Maluku, strengthened the 

percentage of Muslims in the province, but the total number of approximately 100,000 

Muslim transmigrants who settled there between 1969 and 1995 only strengthened 

the Muslim majority in the islands; it did not create it.286 What did change during this 

period, however, was the relative status of Maluku’s Christians. Ever fearful of the 

separatist tendencies demonstrated by the Christians of Maluku since the formation of 

the Republic, highlighted by the continued existence of a Republic of South Moluccas 

(RSM) government-in-exile in Holland, Suharto sought gradually to strengthen the 

Muslim demographic character of Maluku. He provided favorable economic and trade 

advantages to Muslim businessmen operating in Maluku and, with his shift in the early 

1990s to mobilizing Muslim support for his regime, for the fi rst time he appointed a 

284 Ethnologue.com, “Languages of Indonesia (Maluku),” URL: http://www.ethnologue.com/ show_

country.asp?name=IDM. Accessed November 8, 2005.

285 Ambon Information Website, “Population and Religious Breakdown of Maluku,” URL: http://

www.websitesrcg.com/ambon/Malukupop.htm. Accessed November 8, 2005. The data are from the 1995 

Republic of Indonesia census. Data include a caveat that any person not claiming to belong to one of the 

fi ve recognized religions (Muslim, Protestant, Catholic, Hindu, or Buddhist) is classifi ed as Muslim. Seveneighths of Maluku’s Christians are Protestants, and about one-eighth are Roman Catholics.

286 Ambon Information Website, “Transmigration into Maluku,” URL: http://www.websitesrcg. com/

ambon/Transmig.htm. Accessed November 8, 2005.
124

local Muslim governor (Saleh Latuconsina) in Maluku’s provincial capital, Ambon,287

and through a kind of affi rmative action program enabled more Muslims to obtain 

positions in the heretofore largely Christian-dominated provincial administration.288

These factors, along with the May 1998 collapse of the Suharto regime and the 

post-Suharto focus on the revival of democratic processes in Indonesia, perhaps also 

combined with the increasingly aggressive mood of many Indonesian Muslims, seem 

to have led many Maluku Christians to conclude that they were being marginalized in 

Indonesian society, even in their own Maluku homeland. Although historic communal 

tensions had tended to be local and associated with specifi c ethnic or village rivalries, 

general Muslim-Christian tension became apparent in the last months of 1998 and 

fi nally erupted into violence in January 1999. Sparked by a minor quarrel between 

a Christian bus driver and a Muslim immigrant passenger in the Maluku capital of 

Ambon on January 19, 1999, a holiday marking the end of Ramadhan, the Muslim 

month of fasting, the incident escalated into a major street brawl that quickly spread 

to other towns and villages throughout the province. Although no specifi c cause-andeffect relationship can be established, the outbreak of violence in Maluku coincided 

precisely with President B.J. Hababie’s decision to permit a national self-determination 

referendum in East Timor-a decision that upset Muslim opinion in Indonesia but may 

have raised hopes among Christians for similar international intervention on their 

behalf in Maluku.

Evolution of the Crisis 

Although at fi rst perceived as a confl ict between indigenous Ambonese and migrants, 

the confl ict rapidly became a general one between Christians and Muslims in which 

attacks and counterattacks led to the burning of both churches and mosques. It was the 

burning of mosques by Christian gangs that especially outraged Muslim opinion and 

led others to join the Muslim transmigrant communities that were the initial victims of 

the Christian attacks.289 Most sources agree that in the early stages of the confl ict it was 

Christian groups that were on the offensive, with Muslim groups acting in retaliation 

or to defend their communities. Although a lull in the fi ghting occurred in June at the 

time of the national elections,290 it quickly resumed and continued through the end of 

287 Previous appointments had been military offi cers. International Crisis Group (ICG), Indonesia: 

Overcoming Murder and Chaos in Maluku. ICG Asia Report No. 10, December 19, 2000, 2. URL: http://

www.crisisgroup.org/library/documents/report_archive/A400320_19121999.pdf. Accessed August 25, 

2005. 

288 International Crisis Group (ICG), Indonesia: The Search for Peace in Maluku, ICG Asia Report No. 

31, February 8, 2002, 2. URL: http://www.crisisgroup.org/library/documents/report_archive/ A400544_ 

08022002.pdf. Accessed August 15, 2005.

289 International Crisis Group, Indonesia: The Search for Peace in Maluku, 2. In a note the ICG reports 

that when similar attacks broke out on exactly the same day in West Kalimantan (Borneo), Muslim Malays 

had joined with the non-Muslim (Christian) Dayaks in attacks on Muslim Madurese transmigrants. Such 

confl icts were not inherently Christian-Muslim, therefore, but became so in Maluku.

290 International Crisis Group, Indonesia: Overcoming Murder and Chaos in Maluku, 5.
125

the year, at which time offi cial government data indicated that 775 people had been 

killed and 1,108 seriously wounded, while 8,665 houses, 115 churches and mosques, 

and 9,212 shops had been destroyed.291

More signifi cant than these fi gures, however, was the fl ight (in 1999) of 276,446 

(400-500,000 by the end of 2000) refugees, nearly all Muslim transmigrants, many 

returning to the home islands from which they had originated and others into hastily 

erected refugee camps on “safe” islands away from Maluku.292 The aim of the hastily 

organized Christian militias was clearly “ethnic cleansing,” ridding Maluku of as 

many Muslims as possible and staking out areas of territory that could be Christian 

strongholds, as opposed to Muslim stronghold areas that the latter were able to defend 

and cleanse of their Christian inhabitants.

Although vicious attacks were made by both sides, over time the Christian groups 

appeared to have gained the upper hand. Particularly high levels of violence erupted 

in the last week of December 1999, when Muslims burned the largest Protestant (Silo) 

church in Ambon, and partially in retaliation Christians in northern Halmahera island 

“cleansed” the Muslim Tobelo district of 10,000 inhabitants, killing an estimated 400 

or more in the process.293

Until this point, the fi ghting in Maluku was confi ned primarily to the inhabitants 

of the province. The Tobelo massacre, however, coming as it did in the wake of the 

humiliating loss of East Timor in late 1999, stirred emotions throughout the country. 

On January 7, 2000, over 100,000 Muslims in Jakarta held an angry demonstration 

calling for a jihad for the purpose of saving the Muslims of Maluku. Many senior 

Indonesian political fi gures, including Amien Rais, Speaker of the Parliament and 

leader of the Muhammadiyah-based PAN political party, spoke and expressed support 

for the demands of the demonstrators. By the end of the month, various fi ghters 

labeling themselves Laskar Mujahidin began arriving in northern Maluku in direct 

response to the Tobelo Massacre. These fi ghters were having little impact on the 

situation, however.294

Arrival of Laskar Jihad 

In April 2000, a dramatic development was the sudden public appearance of a 

newly organized Muslim militia calling itself Laskar Jihad. Organized and led by 

an ascetic Indonesian cleric of Yemeni (Hadramati) origin, Jaffar Umar Thalib, yet 

291 International Crisis Group, Indonesia: The Search for Peace in Maluku, 2.

292 International Crisis Group, Indonesia: Overcoming Murder and Chaos in Maluku, 26.

293 International Crisis Group, Indonesia: Overcoming Murder and Chaos in Maluku, 8.

294 International Crisis Group, Indonesia: Overcoming Murder and Chaos in Maluku, 8.
126

another veteran of the war in Afghanistan,295 Laskar Jihad received support from 

wealthy Indonesian benefactors, including elements of the Indonesian military.296

Opening recruiting centers in each of Indonesia’s 26 provinces, the new militia rapidly 

emerged as a vehicle for mobilizing popular support for a “peoples’ war” in defense 

of the Muslims of Maluku that the armed forces of the country seemed incapable of 

doing. Training camps were organized at Jogjakarta and on Bogor Island, and on April 

6, 2000, a massive rally was conducted at a large sports stadium in Jakarta, in which 

thousands of Laskar Jihad members participated. The culmination of the rally was 

a march from the stadium to the presidential palace, where Thalib, accompanied by 

thousands of supporters carrying rifl es and machetes and dressed in fl owing white, 

Arab-style thobes, demanded a meeting with President Abdurrahman Wahid. Agreeing 

to see the militia leader, Wahid reportedly exchanged angry words with him in a fi veminute meeting that ended with the President abruptly dismissing him from his offi ce 

and issuing an order for the army to close down the Bogor Island training camp.297

Thalib responded by publicly announcing that 3,000 Laskar Jihad fi ghters would be 

departing Surabaya (East Java) for Maluku on April 29 and 30, in effect challenging 

the government to stop him. Despite the President’s order that Indonesian security 

forces prevent the militia from embarking for Maluku, his order was ignored, and the 

fi rst elements of Laskar Jihad departed Surabaya as scheduled.298 More followed in 

subsequent weeks. 

The arrival of the Laskar Jihad in Ambon had the effect of quickly changing the 

balance of power in Maluku. By mid-June they had joined local Muslim groups in 

offensives against Christian positions and reportedly were receiving the support of 

certain military units.299 One reason Indonesia’s formal security institutions heretofore 

had been unable to contain the violence in Maluku was that they were not large, most 

were locally recruited, and units were confessionally mixed. Christians constituted 

295 International Crisis Group, Indonesia: Overcoming Murder and Chaos in Maluku, 9. Although most 

reports, including this one, identify Thalib as an Afghan war veteran, the International Crisis Group in its 

later 2003 study of the Indonesian veterans (Jemaah Islamiyah: Damaged but Still Dangerous) does not 

include him among its list of those who received training in the Pakistani/Afghan training camps. Certainly 

he claimed to have done so, and also that he had personal relations with Usama bin Ladin. Given that Laskar 

Jihad later emerged as a rival organization of Jemaah Islamiyah, and that Thalib often referred to bin Ladin 

as a “bad” Muslim who did not have a true understanding of Islam, his experience as an “Afghan” jihadi 

certainly led him on a different path than those associated with Jemaah Islamiyah. 296 Elements of Indonesian military reportedly provided Thalib with at least $9.3 million to help him start 

up and organize Laskar Jihad. Ressa, Seeds of Terror, 91, 93.

297 International Crisis Group (ICG), Indonesia’s Maluku Crisis: The Issues, ICG Indonesia Briefi ng 

Paper. Jakarta/Brussels, July 19, 2000, 2 – 3. URL: http://www.crisisgroup.org/library/documents/report_ 

archive/A400113_19072000.pdf. Accessed September 3, 2005.

298 International Crisis Group, Indonesia: The Search for Peace in Maluku, 6. By chance, an American 

journalist, Tracy Dahlby of Newsweek International, on May 22, 2000, boarded the inter-island passenger 

liner M.V. Bukit Siguntang that was carrying Thalib and several hundred of the Laskar Jihad fi ghters as it 

stopped to take on new passengers for Ambon at Makassar, Sulawesi. For an account of his observations, 

see his Allah’s Torch: A Report from Behind the Scenes in Asia’s War on Terror (New York: Harper-Collins 

Publishers, 2005), 11 – 61.

299 International Crisis Group, Indonesia: The Search for Peace in Maluku, 7.
127

approximately 70 percent of the local police forces, whereas military units were 

nearly evenly divided between Muslims and Christians. Both tended to be emotionally 

involved in the confl ict, and their offi cers tended to remain aloof from the confl ict 

in order to avoid a breakdown of discipline and authority in the security services.300

Notably, among the fi rst attacks by the new Laskar Jihad forces was one on the elite 

Police Mobile Brigade in downtown Ambon, designed to go directly at the heart of 

Christian strength in Maluku.301

The Government Reasserts Ascendancy

By late June 2000, the tide had turned, and it was now Christian groups that 

were on the defensive and being made refugees. At this point, on June 26, President 

Wahid who, up to this time had resisted calls to establish martial law-primarily to 

keep the army from regaining lost political infl uence-placed Maluku (which in 1999 

had been divided into two provinces302) under a state of “civil emergency.”303 The 

declaration had no immediate impact on the situation, however, as the Laskar Jihad

offensive against Christian enclaves continued.304 Only after the arrival on August 9 

of a specially created 450-man Joint Battalion (Yon Gab) consisting of special forces 

personnel from the army, navy, and marines did government forces gradually take 

control of the situation. They did so, however, by clashing primarily with Laskar Jihad

and other Muslim elements, thus opening up the government to charges that it, and 

particularly President Wahid, was aligned with the Christian side of the confl ict.

Despite relative government success in imposing security in Maluku by the end 

of 2000, tensions remained high and sporadic attacks by Laskar Jihad on Christian 

enclaves in and around Ambon continued during 2001.305 A result of the violence 

of the previous two years was a clear division of especially southern Maluku into 

mutually hostile enclaves, where inhabitants of each were unable to travel safely 

through the other. Under such circumstances, despite an overall diminution of violence, 

the temporary civil emergency government was unable to take legal action against 

individuals on either side well known to be responsible for various atrocities during 

the previous two years. Without such action, efforts to arrange even an informal ceasefi re, much less reconciliation talks, foundered. Meanwhile, Thalib and other Laskar 

Jihad leaders traveled freely throughout various parts of Indonesia, giving press and 

television interviews and addressing mosque congregations. Taking credit for rescuing 

the Muslims of Maluku from massacre by Christians and for saving Maluku from the 

300 International Crisis Group, Indonesia: The Search for Peace in Maluku, 4.

301 Ressa, Seeds of Terror, 92.

302 A more Muslim northern province called North Maluku, and a more Christian southern province 

called South Maluku. International Crisis Group, Indonesia: The Search for Peace in Maluku, 1.

303 A state of civil emergency, which placed military forces in the provinces under the authority of the 

provincial governors, was a step just short of martial law, which Wahid was loath to declare. International 

Crisis Group, Indonesia: The Search for Peace in Maluku, 8.

304 For details, see International Crisis Group, Indonesia: The Search for Peace in Maluku, 8 – 10.

305 For details, see International Crisis Group, Indonesia: The Search for Peace in Maluku, 12 – 13.
128

fate of East Timor, they were sharply critical of the government both for its relative 

inaction as well as its protection of the Christians of Maluku.306

In an effort to break the impasse, the civil emergency government on April 30, 

2001, arrested Alexander Manuputty, the Christian leader of the Maluku Sovereignty 

Front (FKM — Front Kedanlatan Maluku). The arrest was in response to an April 25 

FKM ceremony recognizing the anniversary of the 1950 declaration of Moluccan 

independence by the Republic of South Moluccas (RSM). In a clear effort to capture 

international attention, both the United Nations and RSM fl ags had been raised, the 

latter still being an illegal act in Indonesia. Although there was no suggestion that 

the Christian leader had been involved in violent action against Muslims in Maluku, 

Manuputty was subsequently sentenced to four months in prison for his offense. Most 

observers agreed, however, that the arrest of Maluku’s most prominent Christian leader 

was in fact done as a prelude to the arrest of Laskar Jihad leader Jaffar Umar Thalib, 

which it did a few days later, on May 4.307

The arrest of Thalib had the impact of transforming him into a controversial, but 

nevertheless national, hero, further undercutting President Wahid’s hold on political 

power. The Muslim political parties-PPP, PBB, PAN, and PK (Justice Party)-all issued 

formal protests of his arrest, as did most of the leading Muslim organizations, such as 

the DDII and KISDI (Committee for Islamic Global Solidarity). Under intense political 

pressure, the government released Thalib from prison on May 15, and on June 12 he 

was released from house arrest, although the charges against him were not lifted. Thalib 

immediately became a prominent television celebrity, denouncing the government for 

its weakness in the face of the “international Christian-Jewish conspiracy” against 

Islam in general and Indonesia in particular. Without the intervention of Laskar Jihad, 

he argued, the fate of Maluku would have been the same as for East Timor.308 The very 

success of Laskar Jihad highlighted the relative impotence of the government and 

contributed to the impeachment process against President Abdurrahman Wahid, led by 

PPP leader Hamzah Haz, that reached its conclusion on July 23. Named Vice President 

in the successor government of President Megawati Sukarnoputri, Haz demonstrated 

the new government’s support for Laskar Jihad by offi cially receiving Thalib in his 

vice presidential offi ce on August 8. 

Close-down of Laskar Jihad 

The July 2001 change of government in Jakarta did not greatly ameliorate the 

situation in Maluku that continues to remain tense until today. The intensity of the 

fi ghting that had characterized the region since early 1999, however, markedly 

declined. Feeling confi dent of its “victory,” Laskar Jihad increasingly focused on 

306 International Crisis Group, Indonesia: The Search for Peace in Maluku, 14.

307 International Crisis Group, Indonesia: The Search for Peace in Maluku, 15.

308 International Crisis Group, Indonesia: The Search for Peace in Maluku, 16
129

religious, educational, and social welfare activities that it claimed had always been 

the central aspect of its mission. Its members continued to be prepared for military 

confl ict, however, and the continuing presence of Laskar Jihad, particularly in the 

southern Maluku capital of Ambon, remained a primary source of continuing tension 

in the islands.309

Following the September 2001 al-Qa'ida attacks in the United States, the question 

immediately arose, particularly in the United States, concerning the possible 

connections between al-Qa'ida and Laskar Jihad. Thalib’s history as a veteran of 

the war in Afghanistan and evidence of visits by “Middle Eastern-looking men” to 

Laskar Jihad locations in Maluku raised natural suspicions. Although Thalib admitted 

he had been offered fi nancial assistance by al-Qa'ida, he adamantly asserted that he 

had not accepted such assistance and took pains to dissociate himself from al-Qa'ida

leader Usama bin Ladin, whom he labeled as being “very empty about the knowledge 

of religion.”310 At the same time, he made use of his television celebrity to sharply 

condemn U.S. military actions in Afghanistan, a stance guaranteed to make him 

perceived by the U.S. administration as a supporter of Usama bin Ladin.

Laskar Jihad remained a highly visible militant Islamic organization operating 

primarily in Maluku, but also in Papua and Sulawesi, until the October 12, 2002, 

Jemaah Islamiyah-sponsored terrorist bomb attack in Bali. Four days later, Thalib 

announced the disbanding of the organization and of his intent to return to teaching 

and writing. A highly publicized withdrawal of 300 Laskar Jihad fi ghters from Ambon 

followed, but it was widely understood that many had elected to stay behind. A new 

outbreak of Christian-Muslim violence in Ambon in April 2004 revealed that these 

had morphed into at least two local organizations — Forum Pemuda Muslim Baguala

and Pemuda Reformasi Maluku.

311 The parent organization of Laskar Jihad, Forum 

Kommunikasi wal Sunnah wal Jummah, moreover, continued to exist and operate with 

offi ces in at least 70 cities throughout Indonesia.312 As a formal, centrally organized 

militia, however, Laskar Jihad had ceased to exist.

SULAWESI AND JEMAAH ISLAMIYAH

Even before the May 2000 arrival of Laskar Jihad fi ghters in Maluku, other 

fi ghters labeling themselves Laskar Mujahidin had made their appearance. Unlike the 

Laskar Jihad organization that numbered at least 3,000 almost from the beginning 

and operated with great publicity, the Laskar Mujahidin in Maluku never numbered 

309 International Crisis Group, Indonesia: The Search for Peace in Maluku, 18.

310 International Crisis Group, Indonesia: The Search for Peace in Maluku, 19. Cf. Abuza, Militant Islam 

in Southeast Asia, 71, and Ressa, Seeds of Terror, 94.

311 International Crisis Groups, Violence Erupts Again in Maluku, ISG Asia Briefi ng, Jakarta/Brussels, 

May 17, 2004, 2. URL: http://www.crisisgroup.org/library/documents/asia/indonesia/ 040517_indonesia_

violence_erupts_again_in_ambon.pdf. Accessed July 15, 2005.

312 Abuza, Militant Islam in Southeast Asia, 72.
130

Map of Sulawesi.

Source: CIA.
131

more than 200 and operated in great secrecy.313 Dressed in black and often wearing 

masks, they were popularly called “ninjas” in contrast to the Laskar Jihad fi ghters 

who wore fl owing white, Saudi-like thobes. Moreover, whereas Laskar Jihad engaged 

in sometimes well-organized direct and indirect attacks on Christian positions, the 

Laskar Mujahidin engaged solely in guerrilla operations-bombings, assassinations, 

and sabotage. Despite assertions by some observers that the mujahidin were mainly 

absorbed by the Laskar Jihad after its arrival in Malaku, the two groups were in fact 

rival organizations that, although they may have had parallel goals, pursued different 

strategy and tactics.314

The Laskar Mujahidin, it later became clear, was in part the creation of Abdullah 

Sungkar’s Jemaah Islamiyah, and more particularly of a collaborating individual, Abu 

Dzar (Haris Fadillah-killed in battle on October 26, 2000 in Siri-Sori Islam, Saparua 

[Maluku]).315 Still a clandestine organization (until revelation of its existence as a 

result of the December 2001 arrests of some of its members in Singapore), Jemaah 

Islamiyah, unlike Laskar Jihad, continued to conceal its existence. The Laskar 

Mujahidin, therefore, remained a very mysterious group until more knowledge about 

it emerged at a later date.

Return of Jemaah Islamiyah 

Following the May 1998 fall of the Suharto regime, Jemaah Islamiyah leaders 

Abdullah Sungkar and Abu Bakar Ba’asyir, taking note of the increasingly chaotic 

political conditions in Indonesia, decided to return to Pondok Ngruki, which they did 

apparently in early 1999. Sometime after his return, Sungkar, believing that the time 

was ripe for a commitment to armed struggle (jihad), met with Achmed Roihan, one 

of the Mantiqi II leaders, and reportedly queried him why such an armed struggle 

had not yet begun. The meeting revealed a fracture in Jemaah Islamiyah between the 

313 International Crisis Group, Indonesia: The Search for Peace in Maluku, 20.

314 International Crisis Group (ICG), Indonesia Backgrounder: How the Jemaah Islamiyah 

Terrorist Newtork Operates, IGC Asia Report No. 43, Jakarta/Brussels, December 11, 2002, 20. 

URL:http://www.crisisgroup.org/library/documents/report_archive/A400845_11122002.pdf. 

Accessed October 11, 2005.

315 Not a member of Jemaah Islamiyah, but of the also underground Darul Islam movement, Fadillah is 

now best known as the father of Mira Augustine, the wife of the alleged Kuwaiti-born al-Qa'ida member, 

Omar al-Farouk (Mahmud bin Ahmad Assegaf). International Crisis Group, Jihad in Central Sulawesi, 

5 – 6. Arrested by Indonesian authorities in Bogor on June 5, 2002, and immediately deported to the newly 

established U.S.-controlled air base in Bagram, Afghanistan, Farouk was a key al-Qa'ida operative who 

had been dispatched with others from Afghanistan in October 1994 by al-Qa'ida leader Abu Zubayda to 

establish a Jemaah Islamiyah training camp, Camp Hudaybiyah, within the confi nes of the Moro Islamic 

Liberation Front (MILF) Camp Abu Bakar. See Romesh Ratnesar, “Confessions of an Al-Qaeda Terrorist,” 

Time, September 3, 2002, 35 – 37, and below, Chapter 6, 209. Later, in 1998, Farouk was transferred to 

Indonesia, where he married the daughter of Abu Dzar. In July 2005, Farouk and others made a daring escape 

from the prison in Bagram. Farouk was believed killed by British forces in Basra (Iraq) on September 25, 

2006. Amit R. Paley, “Al-Qaeda Figure Killed in Raid in Basra, British Military Says,” in The Washington 

Post, September 26, 2006, A16.
132

more idealistic stance of those who had been in exile in Malaysia (Mantiqi I) and the 

more pragmatic realism of those who had remained home in Indonesia (Mantiqi II). 

Roihan replied that human resources were insuffi cient and that further recruitment, 

education, and training were required for Jemaah Islamiyah to move into a phase of 

armed struggle. Sungkar allegedly replied that the time was currently ripe, and it was 

necessary to act now.316

Soon after this encounter, in June 1999, an operational meeting of about 20 Jemaah 

Islamiyah leaders was convened in Solo to discuss the developing crisis in Maluku. The 

meeting was conducted by Jemaah Islamiyah chief of military operations Zulkarnaen. 

A number of those present reportedly criticized Mantiqi II leader Abu Fatih for his 

slowness and bureaucratic approach to taking action. A key result of the meeting was 

the dispatch of Zulkarnaen and several other Afghan veterans, all associated with 

Mantiqi I, to Maluku. The Jemaah Islamiyah group did not conceptualize its mission as 

fi ghting, however, but rather as training. Calling down a number of Jemaah Islamiyah 

fi ghters posted in the Moro Islamic Liberation Front (MILF) training camps on the 

Philippine island of Mindanao, the fi rst Jemaah Islamiyah action was to establish a 

three-month training course on Buru Island for local men and other volunteers desirous 

of confronting the more effectively organized local Christian militias.317

Most of this eclectic group of fi ghters was grouped under the name of another 

organization, Mujahidin KOMPAK (Komite Aksi Penanggulangan Akibat Krisis/Action 

Committee for Crisis Response). KOMPAK was a Muslim charitable organization 

established in 1998 by the DDII “to assist Muslims affected by natural disasters, 

confl ict, and poverty.”318 With the development of the crisis in Maluku, and possibly 

that in East Timor as well, one KOMPAK branch leader in Solo, Arismanandar, a 1989 

graduate of Pondok Ngruki, organized Mujahidin KOMPAK, a subordinate militia 

group initially composed of impatient Jemaah Islamiyah members dissatisfi ed with 

the inaction of the Mantiqi II leadership. Technically separate from Jemaah Islamiyah, 

the distinction was at fi rst more artifi cial than real, probably refl ecting the continuing 

clandestine nature of Jemaah Islamiyah and its policy of not revealing its existence. The 

confusion is compounded by the fact that in training the militia was called Mujahidin

KOMPAK under the leadership of Arismandar, whereas when fi ghting it was known 

as Laskar Mujahidin under the leadership of Abu Dzar.

In the serious battles in Maluku during the summer and fall of 2000, however, the 

Laskar Mujahidin forces were totally overshadowed by those of Laskar Jihad, and by 

the autumn the two groups had fallen into confl ict, a confl ict that refl ected struggles 

316 International Crisis Group, Jihad in Central Sulawesi, 3. Citing the May 9, 2003, interrogation 

disposition of Roihan, ICG Asia Report No. 74. February 3, 2004. URL: http://www.crisisgroup.org/ 

library/documents/asia/indonesia/074_jihad_in_central_sulawesi_mod.pdf. Accessed October 14, 2005.

317 International Crisis Group, Jihad in Central Sulawesi, 4 – 5.

318 International Crisis Group, Jihad in Central Sulawesi, 4.
133

over turf and leadership as well as ideological differences.319 The hegemony of Laskar 

Jihad appears to have led Jemaah Islamiyah/Laskar Mujahidin to fall back on Poso in 

neighboring Central Sulawesi as its main base of operations. Another reason for this 

focus on Poso was the fall in July 2000 of the MILF Camp Abu Bakar in Mindanao 

to the Philippine Armed Forces. The fall of Camp Abu Bakar, which for several years 

had hosted Jemaah Islamiyah Camp Hudaibiyah and al-Qa'ida Camps Palestine and 

Vietnam, meant that Mindanao no longer provided a safe haven for Indonesian and 

other foreign mujahidin. Signifi cant numbers of Jemaah Islamiyah and also al-Qa'ida

trainees began to fl ow back to Indonesia in the summer and fall of 2002, many of them 

fl owing to a new safe haven (al-Qa'ida al-`aminah) in the rapidly growing Jemaah 

Islamiyah/Laskar Mujahidin camp in the mountainous jungles near Poso.320

Strategic Importance of Sulawesi 

Geographically, the island of Sulawesi is the natural logistical, supply, and trading 

route between the southern Philippines and Indonesia, either indirectly via ports in East 

Kalimantan or directly through ports in northern Sulawesi.321 Probably for this reason 

the Jemaah Islamiyah had included Sulawesi as well as all of Borneo along with the 

southern Philippines in Mantiqi III, which it had created in 1997. Northern Sulawesi, 

however, is a largely Christian area, whereas Southern Sulawesi is primarily Muslim, 

while Central Sulawesi-the Palu-Poso corridor that cuts through the middle of the 

island-is a mixed Muslim-Christian region, and Poso, on the east coast of Sulawesi, is 

a natural jumping-off point for supporting military operations in Maluku. Like Maluku, 

although Christians and Muslims in Sulawesi had lived harmoniously for centuries, 

following the collapse of the Suharto regime in May 1998, outbreaks of ChristianMuslim violence in central Sulawesi had become increasingly common. Unlike 

Maluku, however, there was no discernible separatist movement among the Christians 

of Sulawesi. The central issues centered around land disputes and competition among 

the militias of various contending political strongmen, but also resentment toward the 

large number of recent transmigrants from other parts of Indonesia, especially Java, 

that had settled in Sulawesi with the encouragement of the Suharto regime.322

319 International Crisis Group, Jihad in Central Sulawesi, 6. The IGC report notes that the primary 

difference was that, whereas the Jemaah Islamiyah-affi liated militia rejected the legitimacy of the Indonesian 

state, Laskar Jihad saw the purpose of jihad, particularly in Malaku, was solely to defend the state against 

Christian separatists.

320 International Crisis Group, Damaged but Still Dangerous, 23.

321 On the regional transportation networks, see International Crisis Group, How the Jemaah Islamiyah 

Terrorist Network Works, 18 – 19.

322 Human Rights Watch, Indonesia: Breakdown: Four Years of Communal Violence in Sulawesi, III, Part 

One: Context, Causes and Laskar Jihad, 14, 9 (December 2002). URL: http://www.hrw.org/ reports/2002/

indonesia/indonesia1102 – 03#TopOfPage. Accessed November 30, 2005.
134

Splits Within Jemaah Islamiyah 

The Jemaah Islamiyah buildup in the Poso district in late 2000 coincided with 

yet another outbreak of Christian-Muslim confl ict in which Jemaah Islamiyah/Laskar 

Mujahidin fi ghters gradually involved themselves, rapidly translating the confl ict into 

a more purely religious one (jihad). The escalating confl ict in Central Sulawesi at 

this time also exposed signifi cant divisions within Jemaah Islamiyah ranks. The split 

was basically between Jemaah Islamiyah’s trainers and the locally raised Mujahidin

KOMPAC and other trainees. The former insisted on a relatively long training 

period (at least three months) that involved large amounts of religious (ideological) 

instruction designed to produce “educated mujahidin” (mujahadin tertarbiyah) with 

sound understanding of the religious basis of jihad as well as the military skills to 

wage it. The local recruits wanted only military training. Their general attitude was 

expressed by one source as “Enough Quran reading, where’s the war?”323

The situation was made even more complex by the appearance of other separate 

groups that emerged at this time to engage in the confl ict in Central Sulawesi. In 

its report, the International Crisis Group identifi ed at least ten different groups, in 

addition to Jemaah Islamiyah, that were active, sometimes in cooperation and at other 

times in competition and even confl ict with one another.324 The successful example of 

Laskar Jihad in Maluku, which also appeared in Sulawesi in July 2001, clearly had an 

impact on the popular imagination of others who sought to be part of the action. The 

total impact of this complex situation on Jemaah Islamiyah was to limit its recruiting 

efforts and to marginalize it as only one of a number of Islamist groups operating in 

Central Sulawesi.

Transformation of Jemaah Islamiyah 

Jemaah Islamiyah was also impacted by another split within its ranks at this time. In 

November 1999, Jemaah Islamiyah leader Abdullah Sungkar died soon after his return 

from Malaysia to Pondok Ngruki in Solo. He was immediately succeeded by his lifelong 

friend and colleague, Abu Bakar Ba’asyir. Ba’asyir’s assumption of the leadership was 

opposed, however, by some of the younger, more militant leaders of the group who 

viewed Ba’asyir as “too weak, too accommodating, and too easily infl uenced by others” 

and not suitable to continue the legacy of Sungkar.325 Among those opposing Ba’asyir 

included Jemaah Islamiyah operations chief Riduan Isamuddin (Hambali), Abdul 

Aziz (Imam Samudra), Ali Gufron (Mukhlas), and others, all soon to be involved in 

the planning and conduct of signifi cant terrorist operations in Indonesia. The split was 

only aggravated in August 2000, when Ba’asyir and other Islamist leaders convened 

the fi rst meeting of a new organization, the Majelis Mujahidin Indonesia (MMI323 International Crisis Group, Jihad in Central Sulawesi, 8.

324 International Crisis Group, Jihad in Central Sulawesi, 11.

325 International Crisis Group, How the Jemaah Islamiyah Terrorist Network Works, 3.
135

Congress of Indonesian Mujahidin), in Jogjakarta that was attended by approximately 

1,500 individuals.326 Clearly an attempt by Ba’asyir and the other Islamist leaders to 

forge a measure of unity among the proliferating number of radical Islamic groups 

that were springing up in the country in the post-Suharto era, the Jemaah Islamiyah

radicals opposed Ba’asyir’s leadership role in this new organization on the grounds 

that it betrayed Sungkar’s position that the movement should remain underground 

“until the time was ripe to move toward an Islamic state.” Ba’asyir’s view, on the other 

hand, was that the post-Suharto political environment made it necessary for Islamic 

leaders to participate in the political process to achieve this same end.327

Jemaah Islamiyah Launches Operations

It was just at this time, on August 1, 2000, that the Jemaah Islamiyah radicals 

carried out their fi rst terrorist operation in Indonesia, a bombing of the residence of 

the Philippine ambassador in Jakarta. Done in apparent retaliation for the Philippine 

government’s closure of MILF Camp Abu Bakar in Mindanao in July, the operation was 

clearly put together on short notice. Although ordered by Hambali, still in Malaysia, 

it was carried out under the supervision of Fathur Rahman al-Ghozi, Indonesian head 

of Jemaah Islamiyah’s Camp Hudaybiyah within Camp Abu Bakar, who travelled 

to Jakarta in late July for this purpose.328 At the time a totally unattributed event, 

it appeared possibly to have been a Philippine MILF action. Mysteriousness was to 

remain a characteristic of Jemaah Islamiyah terrorist operations until the uncovering 

of the organization in Singapore in December 2001.

The attack on the Philippine ambassador was just a warm-up for the major 

Jemaah Islamiyah terrorist operation yet to come-the Christmas Eve 2000, nearly 

simultaneous, bombings of 38 churches or parsonages in 11 Indonesian cities across 

the country, resulting in 19 deaths and 120 wounded.329 Again, at the time a wholly 

unattributed event, given the continuing Muslim-Christian violence in Maluku and 

Central Sulawesi, the attacks had the appearance of widening the confl ict to include 

all Christians in Indonesia. In fact, the attacks probably were more motivated by an 

effort to demonstrate the presence in Indonesia of a large, well-organized underground 

organization capable of taking actions that no other Islamist group could do.

326 Peter Symonds, “The Political Origins and Outlook of Jemaah Islamiyah,” World Socialist Web 

Site, November 12, 2003,.Part 3, 3. URL: http://www.wsws.org/articles/2003/nov2003/ji3-n14_prn.shtml. 

Accessed February 20, 2005. Also International Crisis Group, Ngruki Network, 17.

327 International Crisis Group, How the Jemaah Islamiyah Terrorist Network Works, 3.

328 For details, see International Crisis Group, Southern Philippines Backgrounder, 18. The report notes 

that there had been an earlier, failed effort to bomb churches in Medan (Sumatra) in May 2000. Ghozi 

returned to the Philippines in October and began organizing a second operation-fi ve nearly simultaneous 

explosions in Manila on December 30, 2000, the so-called Rizal Day bombings. See Chapter 6, .......65....

329 The Christmas Eve bombings are the primary subject of the entire study of the International Crisis 

Group, How the Jemaah Islamiyah Terrorist Network Works. 
136

Formation of Laskar Jundallah

Despite the efforts of the Jemaah Islamiyah radicals to expand the confl ict and 

to assert their own leadership of the Islamist movement in Indonesia, for most the 

attention remained focused on Maluku and Central Sulawesi. In an apparent effort 

to counter the infl uence of the Jemaah Islamiyah radicals, in September 2000 yet 

another militia, the Laskar Jundallah, was established with headquarters in the 

southern Sulawesi city of Makassar (Ujung Pandang). Raised primarily from among 

the Muslims of southern Sulawesi, its founder was Agus Dwikarna, who recently 

had been chosen general secretary of the Majelis Mujahidin Indonesia (MMI) at its 

founding meeting in August. Not a known member of Jemaah Islamiyah, Dwikarna 

was nevertheless a close associate of Abu Bakar Ba’asyir and served at this time as 

head of the Makassar branch of the charitable organization KOMPAK.330 Seen in 

hindsight, the establishment of Laskar Jundallah appears to have been an effort by 

Ba’asyir, working through Dwikarna, to assert his own authority over the Jemaah 

Islamiyah radicals who opposed his leadership.331 Originally conceptualized as a kind 

of religious police that would enforce Islamic law among the Muslims of Sulawesi 

rather than to fi ght against Christians,332 it soon emerged as yet another militia engaged 

in the confl ict in Central Sulawesi.

Laskar Jundallah’s role in the fi ghting would be postponed until mid-2001, however. 

Following the government’s arrest in late July 2000 of Christian militia leader Fabianus 

Tibo,333 and the arrival of augmented government security forces, violence in Central 

Sulawesi diminished signifi cantly over the next year, until a new outbreak of fi ghting 

in June 2001.334 In the meantime, Laskar Jundallah recruits engaged in training with 

Laskar Mujahadin and Mujahidin KOMPAK at their joint training camp located at 

330 For details on Dwikarna, see International Crisis Group, How the Jemaah Islamiyah Terrorist 

Network Works, 31.

331 Dwikarna appears to have used funds from al-Qa'ida, distributed to him through Omar al-Farouk, to 

establish Laskar Jundallah, but soon came to distrust the Arabs who sought to impose a model for jihad that 

was “inappropriate” for Indonesia. International Crisis Group, Damaged but Still Dangerous, 15.

332 International Crisis Group, How the Jemaah Islamiyah Terrorist Network Works, 21.

333 Tibo (age 57 in 2001) was a Catholic immigrant from Flores who emerged as a leader of a particularly 

violent, largely Protestant, Christian militia. On May 28, 2000, he allegedly led a bloody attack on the 

Muslim Wali Songo Pesantren (school) in Poso in which, Muslim sources said, 191 students were killed 

(although only 39 bodies were ever discovered). It was for his leadership of this massacre that he and two 

others were fi nally arrested on July 25. His trial in the early months of 2001 stirred passions on both sides 

and was a contributing factor to renewed Christian-Muslim fi ghting that erupted again in Central Sulawesi in 

June 2001. For details, see Human Rights Watch, Indonesia: Breakdown: Four Years of Communal Violence 

in Sulawesi, IV, Part Two: Chronology of the Confl ict. Study edited by the staff of Human Rights Watch, 14, 

9 (December 2002), 4 – 9. URL: http://www.hrw.org/reports/indonesia/ indonesia1102-04.htmTopOfPage. 

Accessed November 30, 2005.

334 International Crisis Group, Jihad in Central Sulawesi, 13 – 14.
137

Pendola, Pamona Selatan, Poso,335 apparently with the aim of asserting Dwikarna’s 

(and Ba’asyir’s) authority over the mujahidin effort. 

Enter Laskar Jihad

Following the sentencing of Tibo and two of his associates to death in April 2001 

and the failure of their appeal in May, violence again erupted in June. A particularly 

infl ammatory event was the brutal murder of 14 Muslims, mostly women and children, 

by Christian militiamen in the hamlet of Buyung Katedo during the early morning of 

July 3. This led to general fi ghting which even government forces were unable to quell. 

The volatile situation led Jafar Umar Thalib to order about 150 of his Laskar Jihad

from Maluku to “save the situation” in Poso, who arrived in late July. Although small 

in number, they were well-armed with automatic weapons and, as had been the case in 

Maluku a year before, government security forces did nothing to prevent their activities. 

Arriving publicly with great fanfare, the Laskar Jihad presence “reinvigorated the 

confl ict and the sporadic attacks increasingly took the form of organized assaults that 

leveled entire villages.”336

Laskar Jihad’s effort to take command of the situation quickly brought it into confl ict 

with both the Jemaah Islamiyah forces337 as well as government security forces.338

Although the confl ict with the former did not result in fi ghting, Laskar Jihad efforts to 

demonstrate the incompetence of the Jemaah Islamiyah parties led to confrontations 

and name-calling. Confl ict with the security forces beginning in October 2001 did 

lead to bloodshed, casualties, and arrests, apparently due to heightened government 

efforts to assert its authority following the September 11 al-Qa'ida attacks in the 

United States. Government efforts to contain Laskar Jihad, however, led the Islamic 

militia to engage in even fi ercer offensives in November and December.339 Increased 

international criticism of Indonesia, particularly from the United States, which 

worried that the chaotic conditions in Central Sulawesi were precisely those that 

al-Qa'ida was seeking, fi nally led the new Megawati government to take high-level 

interest in the confl ict.

Government Intervention—The Malino Accords

In early December, additional police and army units were sent to Sulawesi “to 

protect vulnerable areas, separate the two sides, conduct mobile patrols, and secure 

335 For a thumbnail sketch of this camp, see International Crisis Group, Jihad in Central Sulawesi, 

11 – 12. The report notes the existence of several camps in the Poso area, but the one at Pendolo was the 

major camp with the most rigorous training program.

336 Human Rights Watch, Chronology of the Confl ict, 14.

337 International Crisis Group, Jihad in Central Sulawesi, 14. 

338 Human Rights Watch, Chronology of the Confl ict, 15.

339 Human Rights Watch, Chronology of the Confl ict, 15 – 21.
138

roads.”340 At the same time, a high-level delegation was appointed to open negotiations 

with the confl icting parties in an effort to end the fi ghting. The delegation was headed 

by Coordinating Minister for Political and Security Affairs, retired General Susilo 

Bambang Yudhoyono (later elected President of Indonesia in September 2004), and 

Coordinating Minister for Public Welfare, Yusef Kalla (later elected Vice President of 

Indonesia in 2004). A particularly key role was played by Kalla, a native of Makassar 

in southern Sulawesi, where he was the owner of a large Toyota auto dealership that 

would become the target of a Laskar Jundallah retaliation bombing one year later on 

December 5, 2002.341

The result of this effort was the so-called Malino Declaration,342 signed by various 

leaders involved in the Central Sulawesi confl ict on December 20, 2001, in the South 

Sulawesi resort town of Malino. Satisfi ed with this process, the two ministers went 

on to apply it in Maluku, reaching the so-called Malino II Agreement on February 12, 

2002.343 Although the two very parallel agreements succeeded in reducing the level 

of violence in both confl ict areas, they did not eliminate it altogether. A feature of 

the negotiation process was the inclusion of only local leaders of both sides and the 

exclusion of the outside groups whom all agreed should be disarmed but permitted 

to continue residing in the confl ict zones. This last provision was suffi cient to gain 

the acquiescence of Laskar Jihad and Jemaah Islamiyah leaders, the latter having 

come to see Poso as fertile ground for the building of a new qa'ida `aminah (secure 

base), “a refuge much like that which Medina became for the Prophet” in early Islamic 

history and as called for in the PUPJI document. A period of peace would facilitate 

this development.344

Post-Malino Sulawesi 

A source of continuing dissatisfaction with the agreement was its failure to assign 

blame for the atrocities committed by both sides. Rather, both agreements promised 

government support and substantial resources for a restoration of the status quo ante, 

the return of all displaced persons to their former places of residence, and government 

funding to replace destroyed homes. Although these provisions as well as the enhanced 

government role in both security and rebuilding activities were suffi cient to end general 

hostilities, a pattern of “mysterious shootings” and “bomb explosions,” primarily 

against non-Muslim victims, continued.345 As a result, the situation in both Central 

Sulawesi and Maluku remained tense and volatile, despite the agreements. Although 

340 Human Rights Watch, Chronology of the Confl ict, 21.

341 International Crisis Group, Damaged but Still Dangerous, 13.

342 Text at Human Rights Watch, Chronology of the Confl ict, 25 – 26.

343 Text at Ambon Information Website, “Mailino II Agreement,” February 12, 2002. URL: http:// www.

websitesrcg.com/ambon/documents/Mailino-II-agreement.htm. Accessed November 6, 2005.

344 International Crisis Group, Jihad in Central Sulawesi, 14.

345 International Crisis Group, Jihad in Central Sulawesi, 16. Appendix C of this report, “Post-Malino 

Accord Violence in Poso,” 28 – 33, provides a full list of these incidents and their perpetrators, if known.
139

government security forces investigated these incidents, they made few arrests until 

after the Jemaah Islamiyah-organized bombing of the Sari nightclub in Denpasar, 

Bali, in October 2002. Naming names, the government apparently reasoned, would 

only undermine the Malino Accord. The Bali bombing, however, demonstrated that a 

more forceful approach was needed.346

Survival of Jemaah Islamiyah

The general cessation of hostilities in Central Sulawesi achieved by the Malino 

Agreement indeed proved to be a boon for the Jemaah Islamiyah in Poso. Permitted 

to remain in the area by the agreement as long as they did not engage in hostilities, 

the organization began to build up its numbers in the Palu-Poso corridor. Already 

in 2001 the headquarters of Mantiqi III had been moved from Camp Hudaibiyah in 

Mindanao to Sandakan (in Sabah, Malaysia) in response to the closure of the former 

camp by the Philippine Armed Forces. Sandakan remained primarily a logistics transit 

point, however, facilitating the movement of arms and men from the Philippines to 

Sulawesi. Throughout 2002, the camp at Pendola, on the shore of Lake Poso in the 

mountains south of Poso City, increasingly became the principal Jemaah Islamiyah

training camp,347 gradually replacing Camp Hudaibiyah in the Philippines. Toward 

346 International Crisis Group, Jihad in Central Sulawesi, 17.

347 International Crisis Group, Jihad in Central Sulawesi, 17 – 20.

Traditional Tongkanan rice barns in southern Sulawesi.

Source: NGA Research Center — Ground Photography Collection.
140

this development Indonesian authorities appear to have cast a blind eye. By the terms 

of the Malino Agreement, as long as it did not engage in hostilities in the two confl ict 

regions, Jemaah Islamiyah was free to build up its organization.

This attitude radically changed following the Bali bombing on October 12, 2002, 

which was quickly attributed to the radical elements of Jemaah Islamiyah.

348 Over the 

next year, more than 90 Jemaah Islamiyah operatives, nearly all affi liated with Mantiqi 

I, were arrested throughout Indonesia for alleged involvement in the Bali bombing.349

These included 12 residing in Central Sulawesi, arrested in Palu in April 2003.350 An 

impact of the increased government pressure was the total end of violence in Central 

Sulawesi until May 2003. The gradual revival of “mysterious killings” and bombings, 

beginning at that time, was attributed to local inhabitants rather than the non-local 

mujahidin groups that continued to maintain a low profi le as well as to disperse to 

other parts of Indonesia.351 Some, such as Laskar Jihad, offi cially disbanded, in part to 

separate themselves from the tactics demonstrated by the Jemaah Islamiyah radicals.

Like Maluku, Central Sulawesi continues to remain tense and volatile. Mysterious 

assassinations and bombings have continued to remain a feature of life in both regions 

in 2004 and 2005,352 creating the odd situation in which violence continues to occur 

despite the general cessation of hostilities that was achieved by the two Malino Accords 

348 Most of the individuals involved in the Bali bombing, it turned out, were associated with Mantiqi I, 

still headquartered in Malaysia, but with many now residing in Indonesia. Almost all were found to have 

been the same men who had carried out the Christmas Eve bombings in 2000. Among them were Hambali 

(who ordered the operation, but was not on the scene); Mukhlis (coordinator of fi nancial and logistical 

requirements); Imam Samudra (fi eld commander on the ground); Dr. Azahari Husin, Dulmatin, and Ali 

Imron (who constructed the bombs and triggered them); Amrozi (purchaser of the explosives); Jimi (suicide 

bomber, driver of the van carrying the explosives detonated outside the Sari nightclub); Iqbal (suicide 

bomber, wearer of an explosive vest who fi rst entered the club and blew himself up before the explosion of 

the van outside); and Idris (detonated a nearly simultaneous, small package bomb outside the U.S. consulate 

in Bali). A total of about 20 individuals were said to have been involved in the Bali bombing. For the full 

story of the Bali bombing, disclosed after the arrest of some of the above individuals, see Ressa, Seeds of 

Terror, 164 – 189.

349 Ressa, Seeds of Terror, 208. The fi rst was Amrosi (arrested November 5, 2002), soon followed by 

Imam Samudra (November 21, 2002) and Mukhlis (December 3, 2002), and fi nally Ali Imron (January 13, 

2003). Others eluded escape, such as Dr. Azahari Husin (killed in a confrontation with police in East Java on 

November 5, 2005) and Dulmatin (believed to still be eluding capture in Mindanao). Hambali was arrested 

by Thai police in Thailand on August 13, 2003. The actual fi rst arrest was MMI and Jemaah Islamiyah

leader Abu Bakar Ba’asyir (October 19, 2002), who denied any knowledge or connection with the bombing 

event. It was Amrozi, owner of the van used in the bombing, who confessed his role and named the others 

involved in the attack.

350 International Crisis Group, Jihad in Central Sulawesi, 20.

351 International Crisis Group, Jihad in Central Sulawesi, 20, 22 – 23.

352 For a list of such incidents in both regions, see Appendix F, “Violence in Poso and Maluku, 

2004 – 2005,’’ in International Crisis Group, Weakening Indonesia’s Mujahidin Networks: Lessons from 

Maluku and Poso, ICG Asia Report No. 103, Jakarta/Brussels (October 13, 2005), 27 – 29. URL: http:// 

www.crisisgroup.org/library/documents/asia/indonesia/103_weakening_indonesia_mujahidin_networks_ 

lessons_fr_maluku_poso.pdf. Accessed December 3, 2005.
141

of late 2001 and early 2002.353 Analysis of this pattern of violence suggests that it is 

largely the product of local mujahidin networks that continue to fi nd Poso and areas 

of Maluku safe havens (qa'ida `amina) in which to live and operate.354 They remain 

engaged in jihad with the Christians of the local areas, thus assisting the government in 

containing potential separatist activity that might emerge from local Christian groups. 

Meanwhile, the higher profi le of government security forces is suffi cient to prevent 

incidents of violence from escalating into wider hostilities. Government actions to 

move against the mujahidin groups have been insuffi cient to bring these perpetrators 

of violence to justice. Nor is such action expected, at least in the short term. In Poso 

and Maluku, at least, the mujahidin groups remain useful adjuncts for maintaining 

Indonesian sovereignty over these potential separatist areas.

PAPUA

When Indonesia gained its independence from Dutch rule in December 1949, 

Netherlands New Guinea (today Papua) was not part of it. Indeed, the remote halfisland remained under Dutch rule until 1963, when as a result of the August 1962 

United Nations-sponsored Dutch-Indonesian “New York” Agreement, it was 

transferred to Indonesian control. Until 1969 Indonesia governed the future province 

as a United Nations Mandate, at which time it was required by the treaty to permit a 

vote on self-determination. In fulfi llment of this requirement, the Suharto government 

“brought 1025 traditional leaders to Jakarta where, under great pressure, they voted 

unanimously on behalf of the people of Papua to join the Republic of Indonesia.”355

The new province was immediately renamed West Irian (Irian Jaya) and, like East 

Timor six years later, incorporated as a province of the Republic.356

From the viewpoint of Indonesian nationalists, such as President Sukarno, who 

considered even Brunei, the Malay peninsula, and southern Thailand as potential 

Indonesian territories and at a minimum all those lands that had been ruled by the 

Dutch, there was no question but that the new province was an integral part of 

Indonesia. Moreover, having abolished voting as un-Indonesian in 1958, when he 

adopted his Guided Democracy concept, Sukarno considered the United Nationsrequired plebiscite a challenge to be fi nessed rather than implemented literally.357 The 

so-called Act of Free Choice of 1969, conducted under United Nations supervision, 

provided suffi cient legitimacy to turn nationalist aspirations into reality, and troops 

originally sent under the command of then Lieutenant General Suharto in 1963 to 

take control of the province ensured that Jakarta commanded the outcome that the 

nationalist leadership desired.

353 International Crisis Group, Lessons from Maluku and Poso, 1.

354 International Crisis Group, Lessons from Maluku and Poso, 3.

355 International Crisis Group, Indonesia: Ending Repression in Irian Jaya, ICG Asia Report No. 23, 

Jakarta/Brussels (September 20, 2001), 3. URL: http://www.crisisgroup.org/library/documents/report_ 

archive/A400414_20092001.pdf. Accessed November 15, 2005.

356 International Crisis Group, Dividing Papua: How Not to Do It, ICG Indonesia Briefi ng, Jakarta/

Brussels (April 9, 2003), 2. URL: http://www.crisisgroup.org/library/documents/report_archive/ A400941_

09042003.pdf. Accessed November 15, 2005.

357 Taylor, Indonesia, 350 – 351.
142

Early Resistance to Indonesian Rule

From the beginning, however, there was resistance. In October 1961, prior to the 

New York Agreement, a committee of leading Papuan members of the New Guinea 

Council had adopted a fl ag (Morning Star) and an anthem (Hai Tanahku Papua), 

together with a political manifesto requesting Dutch recognition of West Papua as an 

independent state.358 In 1964, moreover, following the establishment of the Indonesian 

Mandate, a Free Papua Organization (OPM) had come into being, and the fi rst major 

insurrection against Indonesian rule erupted in Manokwari in 1965. Although the 

OPM never emerged as a sustained insurgent movement as did Fretilin in East Timor, 

it remained a troublesome problem along the border of Papua New Guinea, where its 

fi ghters were able to maintain sanctuary.359

Despite the weakness of the OPM, popular opposition to Indonesian rule was 

general among the native, non-Malay, Melanesian population of the province that as 

late as 1998 constituted about 70 percent of its 1.5 million inhabitants. This percentage 

was signifi cantly reduced from the nearly 98 percent non-Malay population that 

had constituted the province in 1965 because of large-scale government-sponsored 

transmigration from other Islands to Irian Jaya.360 Nevertheless, there long had been 

a small established Malay population, mainly from the eastern islands of Maluku 

and Sulawesi, in the coastal trading towns of West New Guinea. These had remained 

connected to their homes of origin and favored incorporation into Indonesia.361 Their 

numbers augmented by the new transmigrants, these emerged as the new dominant 

economic and political elite of Irian Jaya under Indonesian rule. Generally perceiving 

themselves as part of a higher civilization than the generally more primitive native 

inhabitants, they remained a faithful block of support for Irian Jaya as a part of 

Indonesia. Over a century of Dutch rule, however, had produced a native Papuan, 

largely Protestant Christian, counter-elite that had preferred a continuation of Dutch 

rule or, in its absence, political independence. Although this counter-elite tended to 

collaborate with Dutch rule, serving as members of parliament or in bureaucratic 

positions in Irian Jaya, but especially as church leaders, it continued to symbolize 

Papuan separatist aspirations, particularly in the face of often brutal military efforts by 

the Indonesian government to suppress manifestations of Papuan nationalism.362

The stakes became even higher following the discovery of major copper and gold 

deposits in Papua in the late 1960s. From 1973 on, this meant that Freeport-McMoRan 

Copper and Gold, Inc., the New Orleans-based American company contracted to mine 

these resources, was the largest taxpayer in Indonesia and a major source of revenue 

358 International Crisis Group, Ending Repression in Irian Jaya, 4.

359 International Crisis Group, Ending Repression in Irian Jaya, 2.

360 International Crisis Group, Ending Repression in Irian Jaya, 4 – 5.

361 Taylor, Indonesia, 351.

362 One local human rights activist alleged “921 deaths in Irian Jaya from military operations in the 

period 1965 – 1999.” Friend, Indonesian Destinies, 273.
143

for the Jakarta government. The growing importance of Freeport-McMoRan in Irian 

Jaya and in Indonesian economic life, especially as close Suharto family members 

and friends became major investors, and also the fl ourishing forestry industry of the 

province, raised other issues-especially environmental and economic-that fueled a 

Papuan national movement while at the same time making the Suharto government 

determined to maintain Irian Jaya as an integral part of Indonesia.363

363 International Crisis Group, Indonesia: Resources and Confl ict in Papua, ICG Asia Report No. 39, 

Jakarta/Brussels (September 13, 2002), 17 – 20. URL: http://www.crisisgroup.org/library/documents/ 

report_archive/A400774_13092002.pdf. Accessed November 15, 2005.

Map of Irian Jaya.

Source: CIA.
144

Post-Suharto Revival

As in East Timor and Maluku, the collapse of the Suharto regime in May 1998 led 

to an immediate revival of long-suppressed separatist sentiment in Irian Jaya/Papua. 

Although pro-independence demonstrations in several towns in August were brutally 

suppressed by the army, killing 26, the new reformasi spirit sweeping Indonesia soon led 

a number of Papuan intellectuals, church leaders, and activists to form a new political 

front, the Forum for the Reconciliation of Irian Jaya Society (Foreri). Dissociating 

themselves from the OPM, which they condemned for its violent activities, their stated 

goal was to seek greater autonomy for Papuans to manage their own affairs, either 

through a federal system of government or independence.364 Agreeing to meet with a 

“Team of 100” Papuan leaders designated by Foreri in February 1999, just days after 

his “moment of inspiration” regarding East Timor, new President Habibie was shocked 

to hear that the delegation carried only a single demand — Papua’s independence.365

Habibie made no formal response to the delegation, then or subsequently. The 

unpopularity of his decision to permit a referendum in East Timor virtually ensured 

the adoption of a wait-and-see attitude toward Irian Jaya. The overwhelming rejection 

of autonomy by the East Timorese in August in favor of independence guaranteed that 

no similar experiment would be applied to another province in response to separatist 

sentiments. In any event, by October Habibie was gone, and the problem of how to 

deal with Irian Jaya fell to the new President, Abdul Rahman Wahid.

Rays of Hope under Wahid

The liberal, modernist Wahid immediately acknowledged the former government’s 

errors in Irian Jaya, released political prisoners, and affi rmed the right of all 

Indonesians, including those of Irian Jaya, to freedom of expression, including proindependence demonstrations, as long as they remained peaceful. At the same time, 

however, he made it clear that his government would not accede to Papuan demands 

for political independence.366 A key date was December 1, 1999, the anniversary of the 

1961 formal declaration of Papuan independence. On this day, Papuan nationalists led 

by Theys Hiyo Eluay raised “both the ‘Morning Star’ fl ag in the same place [Jayapura] 

as in 1961, outside the building that had housed the Dutch-established New Guinea 

Council,”367 an act that in previous years would surely have guaranteed arrest on 

charges of rebellion and hero status for those so arrested. On this day, Indonesian 

security forces were absent from the event, a circumstance Eluay described as a 

“miracle.” Efforts the following day by the inhabitants of Timika to raise the fl ag 

364 International Crisis Group, Ending Repression in Irian Jaya, 10.

365 Human Rights Watch, “Violence and Political Impasse in Papua,” A Human Rights Watch Short 

Report, 20, 10(x), (July 2001), 9 – 10. URL: http://www.hrw.org/reports/2001/papers/PAPUA0701.pdf#. 

Accessed December 5, 2005.

366 Human Rights Watch, “Violence and Political Impasse in Papua,” 10.

367 International Crisis Group, Ending Repression in Irian Jaya, 11.
145

again, however, provoked a clash with security forces in which many of the proindependence demonstrators were shot and wounded. The incident and others like 

them led Wahid to pay a personal visit to Jayapura on December 31, 1999, where 

he again assured Papuan leaders “that fl ag-raising and other peaceful expressions 

of pro-independence views would be considered protected acts of free speech,” but 

emphasized that greater autonomy rather than independence was the best Papuans 

could expect from his government.368

Wahid also agreed to the use of state funds to help fi nance a Papuan congress “at 

which, for the fi rst time, Papuan representatives could gather to air their concerns.”369

Two such congresses actually met during 2000. The fi rst, held February 23 – 26, which 

chose a Papuan Presidium Council headed by Theys Eluas, was preparatory to the 

second and main congress, which met between May 29 and June 4. Attended by 

thousands from throughout the province, including many exiles from abroad, but only 

500 offi cial delegates, the second Congress concluded with a resolution stating that 

West Papua (as they called it) had always been a sovereign state since its declaration of 

independence on December 1, 1961; that its incorporation into Indonesia in 1969 was 

“legally fl awed,” and that Jakarta should move quickly to recognize the sovereignty 

and independence of West Papua.370

Swing of the Pendulum

Despite the peaceful political process by which these developments were playing 

out in Irian Jaya, the outbreak of Christian separatist violence in Maluku and ChristianMuslim hostilities in Central Sulawesi during same period, as well as the even more 

powerful separatist movement struggling for independence in Aceh, the apparent 

inability of established security forces to contain the violence, and the emergence 

of popular militia groups such as Laskar Jihad (probably with covert support from 

elements of the armed forces) all contributed to a sense of popular alarm in Jakarta 

and growing disenchantment with the liberal (weak) policies of President Wahid. This 

disenchantment was fi nally refl ected in the Indonesian Parliament (MPR), which in 

August strongly criticized the President’s “accommodative attitude” and ordered him 

to take “decisive actions against separatism and to implement “special autonomy” 

for Irian Jaya and Aceh.371 The action of the Parliament severely undercut Wahid’s 

efforts to reach an accommodating agreement with Papuan leaders and empowered 

the military to resume its traditional hardline policy of suppressing all manifestations 

of Papuan separatism by force.

368 Human Rights Watch, “Violence and Political Impasse in Papua,” 10.

369 Human Rights Watch, “Violence and Political Impasse in Papua,” 10.

370 R. William Liddle, “Indonesia in 2000: A Shaky Start for Democracy,” Asian Affairs, 41, 1 

(January – February 2001), 214.

371 International Crisis Group, Ending Repression in Irian Jaya, 18.
146

Unlike the earlier part of the year, the latter months of 2000 witnessed a number 

of bloody clashes between pro-independence supporters and security forces. In most 

cases, the incident sparking the violence was the simple raising of the Morning Star 

fl ag. The International Crisis Group detailed the main clashes:

Three people were killed in Sorong on 22 August; 34 in Wamena, many 

of them non-Papuan immigrants, on 6 October; fi ve in Marauke on 5 

November; seven more in a clash there on 2 December; three, including 

a policeman, in Abepara on 7 December, with seventeen arrested and 

later tortured.372

As a result of this increased tension, Papuan independence day celebrations on the 

1st of December took place in an entirely different atmosphere from the year before. 

As a precaution, on the day before the observances, police arrested Theys Eluay and 

four other members of the Papuan Presidium Council, charging them with subversion 

because of the role they had played in the congresses earlier in the year. In addition, 

martial law was declared, but organizers of the independence day activities were 

permitted to fl y the Morning Star fl ag-for one day only. The clashes that followed 

represented military efforts to enforce this one-day rule.

Megawati Takes Charge

Meanwhile, a “Crash Program” was set in motion under the leadership of Vice 

President Megawati Sukarnoputri to win Papuans back to support for remaining part 

of Indonesia. The three stated goals of the program were:

Doubling the budget of Irian Jaya to facilitate the development of social and 

economic programs for the benefi t of the native inhabitants.

Removal of all symbols of Papuan nationalism, including vocal leaders, from 

the public arena.

Promoting a Special Autonomy status for Irian Jaya.373

Accordingly, in the tense atmosphere of late 2000 and early 2001, an appointed 

joint committee began work drafting a special autonomy law. “Eleven drafts went 

back and forth between a Papuan team and a parliamentary team” before a fi nal 

version consisting of 79 articles was produced and fi nally adopted by the Indonesian 

Parliament on October 22, 2001.374

Unlike in Aceh, where security forces were less able to assert government authority, 

they were in general able to suppress the pro-independence forces in Irian Jaya that 

372 International Crisis Group, Dividing Papua: How Not To Do It, 5. Human Rights Watch, “Violence 

and Impasse in Papua,” provides a detailed analysis of the incidents in Wamena and Abepura, 11 – 22.

373 International Crisis Group, Ending Repression in Irian Jaya, 18.

374 International Crisis Group, Dividing Papua: How Not To Do It, 6 – 7.

1.

2.

3.
147

had been active in 2000. With the silencing of the generally non-violent independence 

movement represented by Foreri, however, that represented by the OPM (Organisasi 

Papua Merdeka/Free Papua Organization) began to make itself felt again during 2001. 

The kidnapping of three Indonesian transmigrants, employees of a timber company, 

on March 31; the kidnapping of two Belgian fi lm-makers in early June 2001; and the 

killing of fi ve policemen on June 13 were all indicators of this trend. Fierce counterreactions by Indonesian security forces, which included mass arrests, torture, and the 

burning of villages, had the impact of producing nearly 5,000 civilian refugees and the 

complete disruption of economic life in some parts of the province.375

Autonomy for Papua

It was in this atmosphere that Law No. 21 on Special Autonomy for Papua was 

passed by the Indonesian Parliament in October. Megawati, now President of Indonesia 

since the July impeachment of Abdul Rahman Wahid, had planned to attend the 

implementation ceremony for the new law in Jayapura on November 21, but cancelled 

her plans after the November 11 assassination of Papuan independence leader Theys 

Eluays by elements of the army’s special forces (Kopassus). At his trial later, one 

of the Kopassus offi cers affi rmed that he had ordered Eluays’ killing on the basis of 

intelligence that the independence leader, who had denounced the autonomy law from 

the beginning, was planning to make a declaration of independence on December 1.376

The death of Eluays produced a profound shock throughout Irian Jaya and reinforced 

Papuan hatred of the Jakarta regime, while making it clear that the government 

would go to any length to retain control of the province. The new law on Special 

Autonomy, in which Papuan leaders had had signifi cant imput, was suffi ciently farreaching, however, to gain at least the tacit support of a number of previously proindependence leaders. Realizing the determination even of the current administration 

to retain possession of their province, the consensus of many was that the success 

of the new law depended on how effectively it was implemented, not in its specifi c 

provisions. Still others argued that the law could be accepted as a stepping stone 

toward independence-providing practice in self-government that Indonesian authorities 

previously had never tolerated.

The central feature of the law was the establishment of a bicameral legislative 

structure, the upper house (Majlis Rakyat Papua/MRP—Papuan People’s Council) 

being composed only of native Papuans.377 Although only advisory bodies, both houses 

could veto laws or decrees emanating from Jakarta. Now elected rather than appointed 

from Jakarta, but still reporting to the Ministry of Interior, both the governor and 

375 International Crisis Group, Ending Repression in Irian Jaya, 21 – 22.

376 International Crisis Group, Dividing Papua: How Not To Do It, 6.

377 Appointed rather than elected, the MRP was to be composed of one-third community leaders, onethird religious leaders, and one-third women. International Crisis Group, Resources and Confl ict in Papua, 

7.
148

deputy governor were now supposed to be native Papuans rather than appointees from 

elsewhere in Indonesia. The law also renamed the province Papua (not West Papua) in 

deference to Papuan sensibilities, but continued to forbid display of the Morning Star 

fl ag or use of the anthem as instruments of political mobilization. Most importantly, 

80 percent of revenues earned from mining and forestry, and 70 percent from oil and 

gas, were to remain in Papua rather than go to the central government treasury.378 The 

new law also provided for a locally raised constabulary, reporting to the governor, 

that was responsible for security within the province. Army, navy, and air force units 

of the central government could only be deployed in consultation with the provincial 

governor and then only against an external threat, not for domestic security. Control 

of migration in and out of the province was also assigned to “autonomous” provincial 

government. National defense, foreign affairs, and the coinage and regulation of 

money, of course, remained in the hands of the central government. 

All these provisions responded to concrete grievances that Papuan natives had 

been articulating for years. Whether they could be effectively administered by a 

local provincial bureaucracy composed overwhelmingly of non-Papuan Indonesian 

transmigrants remained to be seen. Nevertheless, adoption of the autonomy law had 

the effect of signifi cantly reducing tension during early 2002, as elected (in 2000) 

Papuan governor Jacobus (Japp) Solossa (d. December 2005), a strong supporter of 

the autonomy law, gained increasing popularity throughtout the province because of 

his efforts to increase Papuan involvement in governance and to develop the province 

economically.379

Breakdown of Progress

Several developments toward the end of the year, however, shattered the brief 

interlude of improved Indonesian-Papuan relations brought on by the autonomy law. 

On August 31, 2002, gunmen attacked a convoy of school teachers from the FreeportMacMoRan Company, resulting in the deaths of two U.S. citizens and one Indonesian. 

Made to appear an OPM-type operation, police investigations later implicated 

members of Kopassus, the Indonesian army special forces unit.380 The incident served 

as a pretext, however, for intensive military operations against alleged OPM havens 

378 According to the fi rst Papuan governor, Japp Solossa, these percentages represented an increase 

in the amount of revenues historically available to the provincial government by a factor of about three. 

International Crisis Group, Resources and Confl ict in Papua, 8.

379 Roy Tupai, “Papua Governor Dies, Supporters Suspect Foul Play,” Paras Indonesia, December 20, 

2005. URL: http://www.laksamana.net/read.php?gid=148. 380 Michael S. Malley, “Indonesia in 2002: The Rising Cost of Inaction,” Asian Survey, 42, 1 (January/

February 2003), 141.
149

in Papua.381 Totally in violation of the Law on Special Autonomy, the offensive 

nevertheless was justifi ed as being part of the global war on terrorism.382

A second development was the widely reported appearance of Laskar Jihad fi ghters 

from Maluku in the mainly transmigrant-inhabited coastal towns of Papua. Although 

reports of Laskar Jihad presence occurred as early as 2000, the militia began arousing 

local concern only in December 2001, when its leader, Jafar Umar Thalib, visited 

the newly opened offi ce of its parent organization, the Forum Kummunikasi Ahlus 

Sunna wal Jamaah in Sorong.383 The large infl ux of Laskar Jihad fi ghters, consisting 

of as many as several thousand men, came only in 2002, however.384 They allegedly 

infl iltrated along with a large infl ux of mainly Muslim refugees from the confl ict 

in Maluku. The Laskar Jihad presence in Papua may have been more illusory than 

real, however. Great publicity attended the fi ghters’ arrival in both Maluku in May 

2000 and Poso in July 2001. Such publicity did not accompany their alleged arrival 

in Papua. Rumor and innuendo seemed to be the primary basis of knowledge about 

their presence. Such rumors were perhaps part of a government-sponsored information 

campaign designed to intimidate remaining pro-independence Papuans. On the other 

hand, Papuans themselves, fearful of the cost of rebelling against Indonesian authority, 

may have tended to project their own collective fears onto the reality of the situation. 

According to one Laskar Jihad member interviewed in Papua interviewed in May 

2002, the organization had only seven members in Papua, in contrast to the several 

thousand popularly believed to be there.385

No evidence of Jemaah Islamiyah presence in Papua has been found, although Papua 

was included in the geographical region-along with Australia-as part of the recently 

formed Mantiqi 4. Mantiqi 4 was the last of the four regional structures established by 

Jemaah Islamiyah, although the date of its creation is not yet known. Little is known 

about Mantiqi 4. Most reporting about it comes from Australian sources and refers to 

its activities in Australia, where recruiting, fundraising, and the operation of at least 

381 International Crisis Group, Resources and Confl ict in Papua, 6.

382 In late June 2004, U.S. Attorney General John Ashcroft succeeded in obtaining a federal grand jury 

indictment against Anthonius Wamang, a commander in the Free Papua Movement (OPM), for leading the 

August 31 attack. The indictment contradicted the fi ndings of Papua police chief General Made Pastika that 

elements of the Indonesian military (Kopassus) had in fact carried out the attack. Conn Halliman, “Indonesia: 

U.S. Underwiting Terrorism?” Foreign Policy in Focus (FPIF), September 15, 2004, 1. URL: www.fpif.

org/fpiftext/547. Accessed September 16, 2004. Indonesian authorities, with apparent U.S. FBI assistance, 

fi nally arrested Wamang on January 11, 2006, along with eleven of his associates. Ellen Nakashima and 

Alan Sipress, “Indonesian Arrested in 2002 Slaying of American Teachers,” The Washington Post, January 

12, 2006, A17. Also Ellen Nakashima, “FBI Said Involved in Arrest of 8 Indonesians,” The Washington 

Post, January 14, 2006, A17.

383 International Crisis Group, Resources and Confl ict in Papua, 10.

384 Michael S. Malley, “Indonesia in 2002,” 140 – 141.

385 International Crisis Group, Resources and Confl ict in Papua, 10.
150

two remote training camps appear to have been its primary responsibilities.386 No 

known sources refer to any activities in Papua.

The third development contributing to a new unraveling of Indonesian-Papuan 

relations was a presidential instruction (Inpres) issued by President Megawati 

Sukarnoputri in January 2003 calling for immediate implementation of Law No. 45, 

adopted by the Indonesian parliament in September 1999, which divided Irian Jaya 

into three provinces. In the words of one observer, the instruction did “more to create 

tension and turmoil [in Papua] than any government action in years.”387 The original 

1999 law had been adopted in reaction to the Papuan demand for independence stated 

by the “Team of 100” to President Habibie in January of that year. Clearly aimed at 

countering the Papuan independence drive by means of a “divide and rule” strategy, the 

law nevertheless had not been implemented due primarily to strong Papuan opposition 

and the bias of President Abdul Rahman Wahid to encourage an autonomy process 

rather than measures that would provoke dissent and therefore a more determined 

independence movement. As Megawati, while Vice President, had been the virtual 

architect of the October 2001 autonomy law and had become President by the time of 

its passage and implementation, her action in January 2003 seemed an inexplicable 

reversal of her previous policy.

In any event, Megawati’s instruction also was not implemented. In 2004, Indonesia’s 

Constitutional Court overturned the controversial 1999 law and upheld the Law on 

Autonomy as being in line with the country’s constitution.388 In issuing the instruction, 

Megawati was clearly responding to political pressures from more hawkish elements 

in Indonesia’s government establishment that feared Papuan autonomy, if successful, 

would only be a stepping stone to Papuan independence, a vision that some Papuan 

pro-independence leaders had espoused as well. The KopassU.S.-sponsored terrorist 

incident in August 2002 and the widely believed rumor of signifi cant Laskar Jihad

forces in the province when in fact they probably were few gave evidence of a kind 

of paranoia on the part of some elements of the Indonesian ruling elite that had been 

dismayed by the Law on Autonomy. It was to these elements that Megawati was 

responding in issuing the instruction, despite abundant evidence that such a policy 

would only increase Papuan resentment against Indonesian rule and tended to fuel 

aspirations toward independence.

Papua continues to be a part of Indonesia and will likely continue to remain so 

for the foreseeable future. As has been the case since 1961, however, Indonesia will 

386 Wayne Turnbull, “Mantiqi IV: Australia, Irian Jaya,” in A Tangled Web of Southeast Asian Islamic 

Terrorism: The Jemaah Islamiyah Terrorist Network. Paper written for a graduate study program in 

Southeast Asian Terrorism at the Monterey Institute of International Studies, Monterey, CA, 31 July 2003. 

URL: http://www.terrorismcentral.com/Library/terroristgroups/JemaahIslamiyah/JITerror/Mantiqi4.html. 

Accessed November 14, 2005.

387 International Crisis Group, Dividing Papua: How Not To Do It, 1. This entire article is devoted to 

an analysis of President Megawati’s instruction, its motivation, and its implications. The discussion here is 

based largely on the ICG report.

388 Tupai, “Papua Governor Dies.”
151

continue to face stiff opposition to its rule. Such opposition has endured for more than 

forty years and will not likely be silenced over the short term, except by brute force 

that was characteristic of the Suharto era. Papua will likely remain a problem for 

Jakarta for many years to come.

ACEH AND GAM

By far the fi ercest and most bitter separatist confl ict in Indonesia has been that in 

Aceh, in the far west of the archipelago. Unlike the separatist movements in Maluku, 

Papua and East Timor, which have a Christian-Muslim religious as well as an ethnic 

dimension, however, Aceh is a profoundly Muslim region. Part of its rationale for 

independence, or at least an autonomous status, has been that Indonesia, with its 

Pancasila ideological basis, is widely perceived to be insuffi ciently Islamic for Aceh to 

be a part of it. For this reason, the Acehnese leadership during the early independence 

period, headed by Daud Beureueh, associated themselves with the Darul Islam

Map of Sumatra indicating the Aceh reigion of Indonesia.

Source: CIA.
152

movement, fi ghting to establish Indonesia as an “Islamic state” against the Republican 

forces headed by Ahmad Sukarno. The failure of the Darul Islam movement left many 

Acehnese preferring non-inclusion in Indonesia rather than incorporation within it.

Roots of Acehnese Separatism

An even stronger factor animating Acehnese desires for independence was 

associated with the province’s long history as an independent sultanate. Aceh was 

the last region of the Indonesian archipelago to be brought forcibly under Dutch rule, 

beginning in 1873, and its sultanate was abolished only in 1907.389 Acehnese resistance 

to Dutch rule in fact never ended, and Dutch personnel were being assassinated in 

broad daylight up through the 1930s in Aceh, just prior to the Japanese occupation in 

1942.390 Until conquest by the Dutch, Aceh had never been a taxpaying vassal to any 

of the rajas or sultans of Java. Indeed it was a competing state vying with the rulers of 

Java for suzerain authority over the rajas and sultans of the rest of Sumatra.

Aceh’s geopolitical horizons were also different from those of Java. Its rulers were 

more closely associated through trading relationships and marital ties with the states 

of the Malay penninsula than those of the more distant islands of the Indonesian 

archipelago. Strategically located at the western approach to the Strait of Malaka, it 

was able to threaten shipping lanes to and from India and Arabia and therefore was in a 

position to forge strong diplomatic relations with external powers wishing to maintain 

secure passage through the Straits. With the Portuguese conquest of Malaka in 1511, 

moreover, Aceh emerged as the primary threat to this bastion of European presence in 

the East Indies, and whereas other parts of the Malay world gradually succumbed to 

British, Dutch, and Spanish control, Aceh held out longest among them.

Aceh was also the fi rst region of the East Indies to be impacted by the arrival of 

Islam. Although it eventually became one of many sultanates inhabiting the Malay 

penninsula and Indonesian archipelago, it had pride of precedence and emerged, along 

with Pattani in today’s southern Thailand, as one of the two principal centers of Islamic 

learning in the region. Known regionally as the “threshhold to Mecca” because of its 

historic role as the key departure and return point for pilgrims making the annual hajj

to Mecca, Acehnese in general felt a closer connection to the Arabian heartland of 

the Islamic world than other peoples of the region. The Acehnese court, moreover, 

generally conceptualized itself as the model Islamic government in Southeast Asia.391

389 Taylor, Indonesia, 258.

390 Michael Vatikiotis, “Dissenting History,” Far Eastern Economic Review, 162, 30 (July 29, 1999), 

17.

391 Taylor, Indonesia, 210 – 214.
153

Indonesia Prevails

Given its long independent history, it was perhaps not unnatural that as Holland 

abandoned its imperial claims in the Dutch East Indies in December 1949, Acehnese, 

like many in Maluku and Papua, tended to favor the revival of an independent Acehnese 

state rather than continued subordination to Jakarta. The Indonesian nationalists 

under the leadership of Sukarno and the Sumatran Muhammad Hatta, however, were 

determined to hold Indonesia together as a unitary, centralized state and proved able to 

do so. Under these circumstances, Daud Beureueh, leader of the Acehnese separatist 

movement at the time, threw his lot with the Darul Islam movement. If Aceh were to 

be a part of a greater Indonesia, then it should be on Acehnese terms, an Islamic state 

governed by the shari`a for which Aceh would serve as a model.392

As a result of its rebellion as part of the Darul Islam struggle against the Sukarno 

regime in the early 1950s, however, Aceh was once again subordinated to rule from 

Jakarta by force, a circumstance that ever since has affected its relations with the 

central government. Had Sukarno at this time afforded Aceh with some type of special 

status, as he was later forced to do, many subsequent problems might have been 

avoided. Instead, however, in order to “control” Aceh, he chose to graft it onto a larger, 

newly created province of North Sumatra that relegated historic Aceh to the status of a 

subordinate residency in the bureaucratic structure of the new state. Such a humiliation 

produced continuing resentment in Aceh and contributed to its participation in the 

brief, U.S.-supported North Sumatra rebellion, led by Indonesian Colonel Maludin 

Simholon against the Sukarno regime in 1957.393

Under the able command of the Indonesian army’s Chief of Staff, Abdul Haris 

Nasution, the U.S.-supported rebellions of 1957 – 58 were gradually suppressed,394

and in 1959 Sukarno designated Aceh as a “special region,” where Acehnese “could 

substitute their own laws on religion, custom, and education for rulings from Jakarta’s 

ministries.”395 This status was never confi rmed in law, however, and although Aceh 

392 Richard Chauvel, “The Changing Dynamics of Regional Resistance in Indonesia,” in Indonesia 

Today: Challenges of History, ed. by Grayson Lloyd and Shannon Smith (Lanham, MD: Rowman and 

Littlefi eld, 2001), 152.

393 This rebellion along with others in other parts of Indonesia received U.S. support because of 

Eisenhower administration perceptions that Sukarno’s leadership of the Non-Aligned Movement (NAM) 

was in fact a cover for strengthening Communist world interests in Indonesia. See Friend, Indonesian 

Destinies, 56 – 63.

394 During the period 1952 to 1955, when he was out of favor with Sukarno, Nasution, who had 

commanded Indonesian forces on Java during the revolutionary war against the Dutch as well as against 

the Darul Islam movement, then served as the army’s fi rst chief of staff, wrote Pokok-Pokok Gerilya: Dan 

Pertahanan Indonesia Dimasa Jang Lalu Dan Jang Akan Datang [Fundamentals of Guerrilla Warfare: And 

the Defense of Indonesia, Past and Future] (Jakarta: Pembinbing, 1953). A product of his own experience 

as well as of his studies of the strategies of Mao-Tse Dung and Ho Chi Minh, Nasution’s work has come 

to be considered a classic study of guerrilla warfare and counterinsurgency operations. Friend, Indonesian 

Destinies, 68 – 69.

395 Taylor, Indonesia, 365.
154

remained relatively quiescent during the remainder of Sukarno’s term of offi ce, 

separatist sentiments rapidly reemerged during the Suharto era.396

Aceh Under the “New Order”

Although Acehnese participated enthusiastically in the killing of communists 

following the Gestapu coup against Sukarno, especially those communists of Javanese 

origin in Aceh, and at fi rst appeared supportive of the new Suharto regime, they soon 

became disillusioned with his efforts to forge a Java-centric unitary state. His forcing 

all political activity into two, then later three, offi cial political parties with headquarters 

in Jakarta had the effect of banning all parties having an “Aceh fi rst” platform. From 

1974, all candidates for government positions down to the district level had to be 

approved by the Ministry of Interior in Jakarta and were accountable to that ministry 

rather than to Aceh’s consultative assembly. From 1975, moreover, all government 

offi cials in Aceh were required to be members of Golkar and loyal servants of the ruling 

regime as a condition of employment. Although Suharto placed emphasis on regional 

development, all planning and funding for the building of roads, bridges, schools, 

and industrial infrastructure was accomplished in Jakarta. Technical experts involved 

in regional development, moreover, were employed by the central government and 

were responsible only to it. Industrial zones, conceived of as instruments of national 

security, were controlled either by the military or the Ministry of Interior. `Ulama

were required to be members of the Aceh branch of the national Council of Indonesian

`Ulama and tasked with using their infl uence, through fatwas, to explain and justify, 

not criticize, the wisdom of Jakarta’s policies in Aceh.397

Suharto’s Java-centric policies in Aceh were nowhere more evident than in 

Indonesia’s oil and gas industry, a large portion of which happened to be centered 

in Aceh. Particularly after the 1973 – 74 oil crisis provoked by the October 1973 

Arab-Israeli war, the nearly four-fold increase in petroleum prices helped fuel 

rapid economic growth in Indonesia that continued until the Asian fi nancial crisis 

of 1997. However, the benefi ts of the economic boom fl owed mainly to Jakarta, 

which returned only an estimated fi ve to seven percent of the wealth generated by 

Aceh’s oil and liquefi ed natural gas (LNG) back to Aceh.398 Some saw Aceh’s wealth 

in natural resources as having the potential to transform the province into another 

Brunei, one of the world’s richest states that had retained its independence from 

Malaysia solely by a referendum. As it was, Aceh’s wealth provided more jobs to 

Javanese and foreign workers than to Acehnese. The industrial zones created in Aceh 

for national development, meanwhile, served as modern enclaves for foreign workers 

and Indonesian technocrats who lived a world apart from the impoverished Acehnese 

peasantry living just outside their gates.399

396 Vatikiotis, “Dissenting History,” 17.

397 Taylor, Indonesia, 365.

398 Samantha F. Ravich, “Eyeing Indonesia through the Lens of Aceh,” The Washington Quarterly, 23, 

3 (Summer 2000), 13.

399 Taylor, Indonesia, 365.
155

Revival of Acehnese Separatism and the Formation of GAM

By the early 1970s growing dissatisfaction with Javanese exploitation of Aceh 

became increasingly apparent in two local developments. From the late 1960s, 

efforts led by former Acehnese governor Daud Beureueh to reconsitute the defeated 

Darul Islam were underway. These efforts fi nally bore fruit in 1974 in a formal 

reestablishment of the movement, with Daud Beureueh recognized as imam, or leader, 

of the reconsituted organization.400 Although his role may have been more that of a 

fi gurehead, the real center of the movement being in Java, his readiness to accept the 

leadership role refl ected reborn non-acceptance of Jakarta’s rule in Aceh as it was 

currently constituted.

The reestablishment of Darul Islam was a secret, underground development, 

however. Far more public and dramatic was the announcement two years later, 

in October 1976, of the formation of the Free Aceh Movement (Gerakan Aceh 

Merdaka), or GAM. Much more a classic “national liberation movement,” akin to 

the PULO in southern Thailand or the MNLF in the southern Philippines, GAM was 

animated more by Acehnese ethno-nationalism than by religious ideology, although 

its founder, Hasan di Tiro, openly stated that the Constitution of independent Aceh 

would be the Qur’an.

401

Although GAM was an apparently rival movement of Darul Islam and initially 

drew many of its recruits from the families of former Darul Islam fi ghters, it is perhaps 

noteworthy that it emerged at precisely the same time that Komando Jihad operations 

were getting underway in various parts of Indonesia. As noted earlier, Komando Jihad

was the shadowy operations arm of Darul Islam that had been put together with the 

assistance of Suharto’s intelligence chief, General Ali Murtopu. Murtopu’s support, 

however, had been part of a sting operation that became clear in mid-1977, when 

he ordered the arrest of those Komando Jihad operatives that had become known to 

him.402 Despite the crackdown and witch hunt for Darul Islam members that followed, 

however, Indonesia continued to be bedeviled by Darul Islam-related violence through 

at least the late 1980s.

For the short run, the Suharto government appeared to have dealt more effectively 

with the GAM, which initially was not a deeply rooted movement. Di Tiro (b. 1930), 

who long has made much of his genealogical background as a descendant of the sultans

of Aceh, including its golden age sultan, Iskandar Muda (r. 1607 – 1636), but more 

signifi cantly of Teungu Chik Maat di Tiro, one of the martyred heroes of the Acehnese 

resistance to the Dutch in the late 19th century, had in fact been absent from Aceh for 

400 International Crisis Group, Recycling Militants, 3 – 5.

401 Taylor, Indonesia, 366. Indeed, the formal name of di Tiro’s organization is the Acheh Sumatra 

National Liberation Front (ASNLF), for which the GAM was its military arm. On the ASNLF, see its 

website at URL: https://www.asnlf.net. Accessed January 2, 2006.

402 See above, Chapter 4, 93.
156

many years. Educated in the United States, where he graduated from Columbia and 

Fordham Universities, he became a businessman in New York City until his return to 

Aceh in 1976.

Announcing the formation of GAM, he embarked on his return in October 1976, 

traveling to Bangkok. On October 30, he was smuggled into Aceh and went into 

hiding in the mountains along with a few hundred fi ghters who rallied to his cause. 

On December 4, 1976, a day after the anniversary of the death of his martyred uncle, 

he issued a formal “redeclaration” of Acehnese independence, noting that “Aceh has 

always been a separate country.”403 His revolt posed no grave threat to Indonesian 

authorities, however, which defi ned him as a criminal wanted “dead or alive” and 

conducted a manhunt across the country searching for him. On March 29, 1977, just 

fi ve months after his arrival, di Tiro secretly fl ed Aceh across the Molocca Strait to 

a “neighboring country,” eventually reaching Sweden, where he continues to reside 

today in the southern Stockholm suburb of Nordsborg.404

The Endurance of GAM

The independence movement launched by Hasan di Tiro proved to have more staying 

power than the brief revolt of 1976 tended to indicate, however. In large part, this was 

because of the failure of the Suharto regime to make adjustments to the exploitative 

character of its rule in Aceh. Rather, “Jakarta responded by stationing large numbers 

of troops in the Acehnese province. The result of this throughout the Suharto regime 

was a series of human rights abuses and ongoing political repression by violent means 

through intimidation and organized terrorism which...left deep scars on the psyche of 

the Acehenese people.”405 The policy of subsidizing the out-migration of Javanese 

from overpopulated Java to provincial areas gained particular emphasis in Aceh. As 

it did in Maluku, Papua, and Kalimatan, the transmigration policy, as it was intended 

to do, tended to marginalize native Acehnese and contributed to increasing discontent 

with what was increasingly seen as Javanese imperial rule.

Although GAM remained an ineffectual guerrilla movement throughout the 1970s 

and 1980s, it endured and continued to be a nuisance to government security forces. 

Periodically, di Tiro made surreptitious visits to GAM fi ghters in remote locations in 

Aceh, presumably to bring money and provide moral support. By and large, however, 

he and others focused on international activities, particularly in Europe, publicizing 

the plight of the Acehnese people under Indonesian rule. In the mid-1980s, he achieved 

403 Biographical information drawn mainly from di Tiro’s The Price of Freedom: The Unfi nished Diary 

of Tengku Hasan di Tiro, 1984. Exerpts found at URL: http://www.library.ohiou.edu/indopubs/ 1990/ 

12/19/0012.html. Accessed January 4, 2006. Also Bertil Lintner, “Giving No Quarter: Guerrilla Leader 

Runs Separatist Campaign from Stockholm Flat,” Far Eastern Economic Review, 162, 30 (July 29, 1999), 

19.

404 Lintner, “Giving No Quarter,” 19.

405 Barton, “Islam and Politics in the New Indonesia,” 53.
157

a breakthrough, when he gained the support of Libyan leader Mu’ammar Qadhafi to 

provide military training and support to several hundred Acehnese fi ghters. The return 

of these estimated 500 – 750 fi ghters to Aceh in 1989 sparked new life in the GAM 

revolt. “Armed in part by the Pattani United Liberation organization” (PULO), whose 

own movement in southern Thailand was in a quiescent phase,406 “and in part through 

raids on military outposts, GAM began a series of attacks on local military posts and 

non-Acehnese migrants.”407

The DOM Period, 1990 – 1998

The Indonesian government reacted fi ercely against the new wave of rebellion. In 

May 1990, all of Aceh was declared an area of military operations (daerah operasi 

militer, or DOM), a status it continued to hold until after the fall of the Suharto regime, 

the DOM being offi cially lifted in August 1998 by the new Habibie government. 

Determined to end the insurgency once and for all, the Indonesian military embarked 

on a campaign of violence that made little distinction between members of GAM 

and other Acehnese. Hundreds were killed and buried in mass graves. Many more 

Acehnese were arrested, tortured, and arbitrarily detained for months, sometimes for 

years. Women whose husbands or sons were suspected of involvement or providing 

support to the guerrillas were often raped. The army also burned down houses of 

suspected rebels or sympathizers, sometimes razing entire villages.408

Throughtout 1991, the military conducted public executions of alleged rebels, 

causing many fearful Acehnese to fl ee to Malaysia. Somewhat sympathetic to the plight 

of the Acehnese, the Malaysian government of Mahathir Mohamad refused to return 

these refugees back to Indonesia, when requested to do so by the Suharto regime. 

Despite strong international condemnation of alleged Indonesian military brutalities 

in 1991 – 1992, Indonesia refused to permit journalists or the International Red Cross 

access to the province to investigate and report on the alleged atrocities. In 1992, the 

military affi rmed that the GAM had been totally crushed.409 And so it seemed when 

in the 1992 parliamentary elections Suharto’s offi cial Golkar party won 57 percent of 

the vote in Aceh, up from the typically 40 percent it usually had received in previous 

years.410 By the mid-1990s, support for the GAM appeared to be at an all-time low. 

The continued economic boom, coupled with the repressive measures adopted by the 

government in Aceh, appeared to have eliminated any lingering resistance among the 

inhabitants of Aceh as well as willingness to assist the insurgents.

406 See above, Chapter 3, 70.

407 Ravich, “Eyeing Indonesia Through the Lens of Aceh,” 13.

408 Human Rights Watch, Indonesia: Why Aceh is Exploding. A Human Rights Watch Press Backgrounder, 

August 27, 1999. URL: http://www.hrw.org/campaigns/indonesia/aceh0827.htm. Accessed November 13, 

2005.

409 Andrew Tan, “Armed Muslim Separatist Rebellion in Southeast Asia,” Studies in Confl ict and 

Terrorism, 23 (October/December 2000), 278.

410 Indonesia: A Country Study, 227.
158

After Suharto

How wrong this assessment was became evident immediately after the fall of 

the Suharto regime in May 1998. The new thrust toward democratic change was 

accompanied by a liberalization of the press that previously had been a mouthpiece of 

the Suharto regime. Throughout the summer of 1998, newspapers and nightly television 

broadcasts were fi lled with revelations of atrocities committed by the military forces 

in Aceh as well as East Timor and other parts of the country. A strong mood emerged 

that the DOM should be lifted, military forces withdrawn from Aceh, the perpetrators 

of crimes persecuted, and victims compensated.

Accordingly, on August 8, 1998, following a formal apology to the people of Aceh 

for all they had endured at the hands of the military, General Wiranto, Chief of Staff 

of the Indonesian Armed Forces, offi cially lifted the DOM and stated that all combat 

forces would be withdrawn from Aceh by the end of the month. At the formal ceremony 

on August 31 marking the fi nal troop pullout, however, cheering Acehnese jeered and 

pelted the withdrawing troops with stones. The violence quickly turned into a fullscale riot in the oil and gas center of Lhokseume. Although many Acehnese believed 

the troubles had been initiated “by departing troops unhappy at being taken away 

from their lucrative sources of income from illegal logging and marijuana cultivation 

in Aceh,” charges that were never investigated, the riot caused the troop withdrawal 

to be promptly reversed. In justifying his new decision, General Wiranto stated that 

withdrawal depended upon the good behavior of the people of the province.411

It quickly became apparent, however, that in the new post-Suharto political 

environment GAM, which originally had lacked deep popular support, had now 

become a grassroots movement, largely because of “deep-seated resentment and 

growing hostility toward the military’s abuse of power.”412 As instances of violence 

multiplied, many Acehnese fl ocked to the GAM, as the military began to return to 

Aceh and to renew its brutal campaign to contain the revived insurgency. Despite 

the apparent good will of August, the year ended in a paroxysm of violence, as GAM 

forces renewed their attacks on government installations and Javanese migrants, and 

the army responded with indiscriminate attacks on villages thought to harbor GAM 

“terrorists” or to be sympathetic to the GAM.

Impact of the East Timor Referendum

Yet another critical shift occurred following the January 27, 1999, announcement 

by President B.J. Habibie that East Timor would be permitted to have a referendum on 

the question of autonomy or independence. Almost immediately an all-Aceh student 

411 Human Rights Watch, Indonesia: The War in Aceh, A Human Rights Watch Report, 13, 4 (August 

2001), 8. URL: http://www.hrw.org/reports/2001/aceh/indacheh0801.pdf. Accessed November 13, 2005.

412 Ravich, “Eyeing Indonesia Through the Lens of Aceh,” 13.
159

congress called for a similar referendum in Aceh. This was followed by the formation 

of a province-wide, student-led Information Center for a Referendum on Aceh (Sentral 

Informasi Referendum Aceh, or SIRA). SIRA presented itself as an alternative to GAM, 

arguing that a referendum would be a peaceful way to end the confl ict rather than the 

violent path followed by GAM.413

Although there were at fi rst no known links between SIRA and GAM, their 

objectives were closely parallel, and both movements experienced great success during 

1999 mobilizing popular support, despite brutal efforts of Indonesian security forces to 

disperse pro-independence demonstrators and track down GAM fi ghters. While SIRA 

demonstrated in November 1999 that it could organize a peaceful gathering of more 

than 500,000 Acehnese in support of a referendum, GAM began in various districts 

where it could to organize village councils loyal to its leadership, rather than that of 

the central government, and to collect taxes that enabled it to buy arms from various 

markets.414 According to one observer, by mid-2000 GAM controlled as many as half 

the villages in the province.415

Part of the reason for the growing success of the Acehnese independence movement 

at this time was clearly the large discrepancy between the policy orientations toward 

Aceh of Jakarta’s new political leadership and the military which retained the strong 

support of the Parliament. Whereas President Habibie in a March 1999 visit to the 

Acehnese capitol, Banda Aceh, had formally apologized for past abuses by the military 

and in June appointed an Independent Commission to Investigate Violence in Aceh, he 

was not able to deliver any positive result prior to his electoral defeat and replacement 

by President Abdurrahman Wahid in October. Wahid, meanwhile, when campaigning 

in Aceh, had stated that he favored the desired referendum, leading many to believe 

that it would be forthcoming following his election.416 Wahid too proved unable to 

deliver on his promise, due primarily to parliamentary as well as military opposition. 

For a brief moment, though, the fragmented politics of Jakarta gave hope to proindependence forces in Aceh that their movement contained the promise of success.

Wahid’s Opening to GAM

Unable to risk his limited political capital by permitting a referendum in Aceh, 

particularly after the overwhelming rejection of Jakarta’s rule by the August 1999 

referendum in East Timor, Wahid instead toward the end of 1999 sent an envoy to 

Stockholm to open a dialogue with GAM leader Hasan di Tiro. Although di Tiro rejected 

this overture after Wahid announced it publicly, he did authorize GAM representatives 

to meet with Indonesia’s ambassador to Switzerland and the United Nations, Dr. Hasan 

413 Human Rights Watch, Indonesia: The War in Aceh, 9.

414 Human Rights Watch, Indonesia: The War in Aceh, 10.

415 R. William Liddle, “Indonesia in 2000: A Shaky Start for Democracy,” Asian Survey, 41, 1 (January/

February 2001), 213.

416 Friend, Indonesian Destinies, 477.
160

Wirajuda, under the auspices of the Henry Dunant Center for Humanitarian Dialogue in 

Geneva.417 This meeting initiated a negotiation process that fi nally led to a three-month 

“humanitarian pause” agreement between GAM and the Indonesian military in May 

2000 that continued to be extended until it fi nally broke down in July 2001.418

Not quite a complete cease-fi re, the agreement did produce a signifi cant decline in 

violence for several months. The lull in the fi ghting, whose purpose was to permit a fl ow 

of humanitarian aid to the people, nevertheless, provided an environment in which the 

GAM was able to expand its control in the countryside.419 These advances Indonesian 

forces tended to counter violently, while GAM responded with counterattacks. As 

outbreaks of fi ghting soon resumed, monitoring teams operating under the agreement 

tended to keep the fi ghting in check. Nevertheless, total deaths from fi ghting escalated 

from an estimated 400 in 1999 to nearly 800 in 2000.420

A particular strategy adopted by GAM at this time was to target ExxonMobil’s oil 

and gas production and refi nery facilities at Lhokseume, on Aceh’s northern coast. 

These facilities, located in an area where the fi ercest insurgency activity was occurring, 

produced about 32 percent of the total value of Indonesia’s oil and gas production and 

generated about $1.43 billion per year (in 2000) in foreign currency. Sniping, kidnapping, 

murder, arson, trespassing, and robbery, mainly against individual employees of the 

company, were all techniques used to increase the level of insecurity experienced by 

ExxonMobil employees. The strategy had its desired effect, when in March 2001 the 

company announced the closing down of its operations in Aceh. The shutdown, which 

417 Rohan Gunaratna, “Aceh Rebels Agree to Extend Ceasefi re,” Jane’s Intelligence Review, 13, 3 

(March 2001), 4.

418 The texts of all the agreements between the Indonesian government and the GAM can be found on 

the Dunant Center (now called the Humanitarian Dialogue Center) web site at URL: http://www. Hdcentre.

org/?aid=153. Accessed January 16, 2006.

419 United States-Indonesia Society (USINDO), “National Integration in Indonesia: The Cases of Aceh 

and Papua.” Remarks by Ambassador Wiryono Sastrohandoyo. USINDO—East-West Center Washington 

Joint Forum. (October 1, 2002). URL: http://www.usindo.org/Briefs/Joint%20USINDO-EWC%20on%20

Aceh%20and%20Papua.htm. Accessed January 16, 2006. It was at this time, in June 2002, just after the 

May “humanitarian pause” agreement under which two al-Qa'ida leaders, Muhammad Atef and Ayman 

al-Zawahiri, visited Indonesia, stopping fi rst in Aceh and then moving on to Maluku. They were escorted 

during their visit by al-Qa’ida representative in Indonesia Omar al-Farouk and South Sulawesi Islamic 

leader Agus Dwikarna, who later in the year would participate in the establishment of the Majelis Mujahidin 

Indonesia with Jemaah Islamiyah leader Abubakar Ba’asyir and others and also of Laskar Jundallah, a new 

militia aimed at enforcing Islamic law in Southern Sulawesi. According to Abuza, the purpose of the alQa'ida visit was “to establish a base area and training facilities in Indonesia, to complement Afghanistan.” 

Abuza goes on to say that although Zawahiri and Atef were favorably impressed by the situation in Aceh, 

“GAM resisted their overtures and al-Qaeda did not establish a base in Aceh.” Abuza, Militant Islam in 

Southeast Asia, 149, 160, 176. A more likely interpretation of the meaning of this visit was to see how alQa'ida could assist the GAM rebels. The move to expand control of the countryside, establish an improved 

tax base, and purchase more weapons, most of which seemed to come from arms markets in Thailand and 

Cambodia through Malaysia, in which Jemaah Islamiyah may have played an important intermediary role, 

seems to have dated from this visit.

420 CNN, “Aceh: A Timeline of Insurgency,” CNN.com web site. URL: http://www.cnn.com/2003/ 

WORLD/asiapcf/southeast/05/19/acehtimeline/. Accessed September 19, 2005.
161

lasted until July, had a devastating economic impact on Indonesia, still reeling from the 

1997 Asian fi nancial crisis, when it forced the company’s biggest customers-especially 

Japan and South Korea-to seek other sources for their oil and gas supplies.421

Although GAM’s strategy seemed counterproductive to many, a key grievance of proindependence Acehnese was Jakarta’s expropriation of nearly 95 percent of the revenues 

earned from Aceh’s oil and gas production for use elsewhere in the country rather than 

Aceh. The forced closure of ExxonMobil, therefore, harmed the government far more 

than it did the local Acehnese economy. Moreover, it demonstrated the inability of 

Indonesian security forces to provide the security necessary for the company to maintain 

operations without local Acehnese cooperation.

Resumption of the Confl ict

Despite President Wahid’s preference for a negotiated settlement, he found himself 

with no choice but to authorize a renewed military campaign in Aceh, which he did 

in April.422 At the same time, in July, he obtained from the parliament a new law that 

granted Aceh’s provincial government 70 percent of revenues from natural gas exports, 

the right to hold direct elections for local offi cials, to raise its own police force, and 

authority to implement Islamic law. This basic grant of autonomy was considered 

insuffi cient by most Acehnese, however, for whom independence had now become a 

deeply rooted demand. As a result, the new law failed to receive a positive response and 

fi ghting continued, 2001 being the bloodiest year to date in the history of the confl ict, 

with nearly 1,500 recorded deaths by year’s end.423 In July, as ExxonMobil resumed 

operations in Lhokseume, the government withdrew from its dialogue with GAM in 

Geneva as well as participation in the joint monitoring teams tasked with investigating 

outbreaks of violence. Government forces also started arresting Acehnese members of 

the monitoring teams, setting off a fl urry of GAM retaliatory actions through the rest of 

the year.424

Even this reversal of his former conciliatory policy did not save the presidency 

of Abdurrahman Wahid, however, who was impeached on July 23 on grounds of 

incompetence and corruption. His successor, Megawati Sukarnoputri, although she too 

suffered from limited support in both the parliament and the military, nevertheless was 

very hardline on maintaining the unity of Indonesia, which she saw as a legacy of her 

father. In the interest of maintaining this unity, she strongly supported the autonomy 

law for Aceh, which she signed into effect on August 11, 2001, and which immediately 

421 John McBeth, “Too Hot to Handle: Why ExxonMobil Closed Down Onshore Gas Fields in Aceh,” 

Far Eastern Economic Review, 164, 12 (March 29, 2001), 16. Also Paul Harris, “No Solution in Sight in 

Anarchic Aceh,” Jane’s Intelligence Review, 13, 5 (May 2001), 30.

422 Malley, “Indonesia in 2001,” 128.

423 Malley, “Indonesia in 2001,” 128.

424 Human Rights Watch, “Indonesia,” Human Rights Watch World Report 2002, 6 – 7. URL: http://www.

hrw.org/wr2k2/asia7.html. Accessed December 12, 2005.
162

became the centerpiece of her policy in Aceh.425 Correctly perceived as an “imposed” 

policy from Jakarta by pro-independence elements in Aceh, it gained little support in 

the province, where the struggle for independence continued. The intensity of military 

action increased accordingly as the offi cial position of the government hardened into 

a stance of “autonomy or nothing.”426

Impact of 9/11

At this juncture, the al-Qa'ida-sponsored, September 11, 2001, attacks in the United 

States intervened to change the international climate in which the confl ict with Aceh 

was taking place. United States efforts to improve relations with Indonesia and to 

solicit its support in the global war on terrorism led Megawati to link publicly GAM 

with Islamic terrorism, despite the lack of strong evidence that could be marshaled to 

demonstrate such a linkage. U.S. policymakers, however, although they urged a peaceful 

resolution of the Aceh confl ict through negotiations, also continued to express support 

for the continued “territorial integrity of the Republic of Indonesia.”427 In contrast to 

the earlier East Timor confl ict, the international climate favored the position of the 

Indonesian government in Aceh rather than that of the pro-independence forces.

“Cessation of Hostilities”

Realizing that the negotiating process it had been mediating was disintegrating, 

in early 2002 the Henry Dunant Center (HDC) in Geneva sought to revive it by 

involving three particularly infl uential international “wise men.” The three were retired 

American Marine General Anthony Zinni, known to have a personal relationship with 

U.S. President George W. Bush as well as State Department sanctions for working 

with the HDC; Dr. Surin Pitsuwan, former Muslim foreign minister of Thailand 

and currently active as Thai representative in ASEAN; and former Yugoslav foreign 

minister Budimir Loncar, who had been Yugoslavia’s ambassador to Indonesia during 

the Sukarno regime and remained close to the Sukarno family. Traveling extensively 

during 2002, meeting GAM and Indonesian government representatives, and working 

with their respective constituencies-Zinni with the U.S. government, Pitsuwan with the 

ASEAN foreign ministers, and Loncar particularly with President Megawati-the team 

ultimately succeeded in leading the two parties into signing a “Cessation of Hostilities 

Framework Agreement” in Geneva on December 9, 2002.428

425 Human Rights Watch, “Indonesia,” Human Rights Watch World Report 2002, 7.

426 Kira Kay, “The ‘New Humanitarianism’: The Henry Dunant Center and the Aceh Peace Negotiations,” 

WWS Case Study 2/03, Princeton University, Woodrow Wilson School of Public and International Affairs 

(February 2003), 7. URL: http://www.wws.princeton.edu/cases/papers/newhumanit. html. Accessed January 

17, 2006.

427 Kira Kay, “The ‘New Humanitarianism,’” 7.

428 Text at HDC website, URL: http://www.Hdcentre.org/?aid-153. Accessed January 16, 2006.
163

The task of the three “wise men” was not an easy one because, after the signing of 

the autonomy law on Aceh in August, the policy of the Megawati government was to 

forego continued negotiations with the GAM in favor of imposing the law by force, 

although it remained open to discussions with GAM if the rebel organization formally 

accepted the autonomy law, rather than independence, as the “end point” of the 

negotiating process.429 Unable to obtain such a commitment from GAM spokesmen, 

fi ghting continued throughout the year, as the military, whose forces amounted to 

nearly 30,000 as opposed to 4,000 GAM rebels, intensifi ed its pressure in Aceh. Over 

the course of the year, the GAM forces were gradually driven back into mountain 

and jungle retreats where they remained effectively surrounded by elements of the 

Indonesian military, thereby losing control over the territories and districts GAM had 

come to dominate during the previous year.430 Meanwhile, estimated deaths for the 

fi ghting during 2000 were 1,230 persons, mainly civilians rather than combatants from 

either side.431 Within this context, the mediated settlement of December 9 appears 

to have been reached on the basis of three principles laid down by the mediating 

team: (1) International community respect for the territorial integrity of Indonesia 

and non-support for the independence of Aceh; (2) Indonesian acceptance of 

international monitors to oversee implementation of the agreement; and (3) restoration 

of U.S. military and economic assistance to Indonesia, severed since the East Timor 

crisis of 1999, only in response to a satisfactory settlement of the Aceh confl ict.432

Although the term “autonomy” did not appear in the cease-fi re agreement, a provision 

mandating early elections (independently set for April 2003) in terms of the autonomy 

law of August 2002 implied its acceptance by GAM. Moreover, a central role for 

a reconstituted Joint Security Committee, comprised equally of GAM, Indonesian, 

and international (mainly Thai) members to report on violations of the cease-fi re, was 

meant to ensure adherence by both parties to the terms of the cease-fi re agreement.

Fighting Resumes

The ink was barely dry on the new agreement when fi ghting erupted again. As had 

been true after the May 2000 “humanitarian pause,” GAM was perceived to be taking 

advantage of the lull in fi ghting to rearm and recover its strength,433 and Indonesia 

responded by renewing the fi ghting. In April 2003, Megawati cancelled the scheduled 

election mandated by both the cease-fi re agreement and the autonomy law and also 

broke off further talks with the GAM. On May 19, the government once again declared 

martial law in Aceh. Troop strength in the province was raised to approximately 45,000, 

and a full-scale offensive was ordered to eliminate the 3,000 – 5,000 GAM fi ghters 

429 Malley, “Indonesia in 2002,” 140.

430 Tom Farrell, “Hopes for Aceh Ceasefi re,” Jane’s Intelligence Review, 14, 8 (August 2002), 47.

431 Human Rights Watch, “Asia: Indonesia,” Human Rights Watch World Report 2003, 4. URL: http://

www.hrw.org/wr2k3.asia7.html. Accessed December 5, 2005.

432 Kira Kay, “The New Humanitarianism,” 8.

433 Jamie Miyazaki, “Aceh Talks Raise Hopes for Settlement,” Jane’s Intelligence Review, 17, 4 (April 

2005), 23.
164

once and for all.434 Although army offensives pushed GAM forces into the mountains 

and eastern portions of Aceh, greatly weakening their operational capabilities, they 

remained far from defeated after two more years of war. Meanwhile, hostilities 

resulted during the period May 2003 to December 2004 in an estimated 2,300 deaths 

and upward of 125,000 – 150,000 internally displaced refugees living in deplorable 

conditions.435 Most external observers doubted that the GAM could ever be totally 

defeated. At best, it could be keep in an isolated condition, but only at a prohibitive 

cost to the government.

Impact of the Tsunami

The devastating tsunami that hit Aceh’s western coastline and destroyed most of the 

capital, Banda Aceh, on December 26, 2004, totally altered the context in which the 

confl ict was perceived by all parties. Of a total population of about four million people 

in Aceh, the tsunami resulted in approximately 200,000 deaths and more than 800,000 

displaced persons.436 The requirements for international humanitarian assistance were 

overwhelming, and the international community was quick to respond with massive 

infusions of humanitarian relief. The Indonesian government, meanwhile, unable to 

cope with the crisis alone, opened the region to international aid and human rights 

workers who previously had not been permitted access to the province because of the 

exigencies of the war. For its part, GAM, from its headquarters in Stockholm, called 

for an immediate cease-fi re so that relief supplies and aid personnel would not be 

hampered by insecurity.437 For a few weeks, the large Indonesian military presence 

in Aceh did scale back operations against the GAM as it sought to cope with the 

immensity of the humanitarian crisis (many Indonesian soldiers also lost their lives 

in the tsunami) and also to assert control over the international relief effort. Soon, 

however, skirmishes resumed, with the military claiming to have killed as many as 200 

GAM rebels in January 2005.438

Yudhoyono’s Preference for Negotiations

New political leadership in Jakarta also had a signifi cant impact on the post-tsunami 

political environment in Aceh. In October 2004, Susilo Bambang Yudhoyono had 

replaced Megawati Sukarnoputri as President of Indonesia and had brought with him as 

his vice presidential running mate Yusef Kalla, a wealthy South Sulawesi businessman 

434 Rita Smith Kipp, “Indonesia in 2003: Terror’s Aftermath,” Asian Survey, 44, 1 (January/February 

2004), 67.

435 Brad Adams, “Aceh’s Forgotten Victums,” Jakarta Post, May 27, 2005. URL: http://www.hrw.org/

english/docs/2005/27/indo11069. Accessed January 17, 2006.

436 Edward Aspinall, “Indonesia after the Tsunami,” Current History, 104, 680 (March 2005), 105.

437 Centre for Humanitarian Dialogue, “Acahe, Indonesia-Latest Update,” HD Centre for Humanitarian 

Dialogue Website, undated. URL: http://www.Hdcentre.org/?aid=44. Accessed January 17, 2006.

438 Anthony L. Smith, “Aid Efforts in Aceh Encourage Peace Talks,” Jane’s Intelligence Review, 17, 3 

(March 2005), 40.
165

and important member of Golkar.439 As former ministers in Megawati’s government, 

the two had been key facilitators of the two Malino Agreements of December 2001 and 

February 2002 that had gone far to defuse separatist sentiment and sectarian confl ict in 

Sulawesi and Maluku respectively. They would soon do so in Aceh as well.

A retired military offi cer, who subsequently had served in several cabinet positions, 

Yudhoyono cultivated the image of a strong leader interested only in effective and 

effi cient government. During his fi rst year in offi ce, moreover, he gained much popular 

credit for cultivating Indonesia’s democratic institutions-fair local elections, a free 

press, respect for the parliament, and a concerted effort to crack down on corruption.440

Regarding Aceh, the new President early on indicated that only a negotiated rather 

than an imposed settlement could end turmoil in the province. The lead in this effort, 

however, was undertaken by Kalla who, following the tsunami “was the fi rst senior 

offi cial to visit Aceh, fl ying over the devastated coastal fringe in his private jet.”441

Kalla’s assumption of leadership in the Aceh crisis and in subsequent negotiations with 

the Acehnese led to speculation that he rather than the President was “actually running 

the show,” rumors that Yudhoyono sought to set aside by saying, “Nothing that is done 

by the vice president is unknown to me.”442 Others speculated that the hard-headed 

businessman from Makassar was motivated primarily by securing contracts for housing 

and infrastructure reconstruction in Aceh for his own companies as well as those of his 

key political allies.443 Nevertheless, the sincerity of the new administration’s policy 

toward a negotiated settlement was probably best expressed by the replacement in 

early 2005 of Army chief of staff General Ryamizard Ryncuda, who openly opposed 

the reopening of negotiations with the GAM just at the moment the armed forces were 

on the edge of victory and a total capitulation of the GAM.444

GAM’s positive response to the overtures of the government was probably due less 

to the effects of the tsunami on Aceh than to the new international spotlight that had 

been placed on Aceh as a result of the tsunami. With the infl ux of international media, 

thousands of international aid workers, and hundreds of foreign offi cials monitoring the 

relief effort, the plight of the inhabitants of Aceh had in fact become internationalized, 

long a strategic goal of GAM. With Aceh fi nally having international visibility, GAM 

439 Making use of his new offi ce as Vice President, Kalla won control of Golkar at its national congress in 

December 2004, shortly before the tsunami disaster. By assuming leadership of the party, he transformed the 

opposition party it had become since the fall of Suharto back into a party that was part of the ruling coalition. 

Aspinall, “Indonesia after the Tsunami,” 107.

440 Michael Vatikiotis, “Yudhoyono’s First Year: Striking the Right Balance,” The Straits Times, October 

4, 2005. URL: http://www.worldsecuritynetwork.com/printArticle3.cfm?article_id=11989. Accessed 

November 6, 2005.

441 Aspinall, “Indonesia after the Tsunami,” 107.

442 Michael Vitikiotis, “Yudhoyono: Indonesia’s Man in Charge,” International Herald Tribune, February 

17, 2005. URL: http://www.worldsecuritynetwork.com/printArticle3.cfm?article_id=10981. Accessed 

November 6, 2005.

443 Aspinall, “Indonesia after the Tsunami.” 108.

444 Jamie Miyazaki, “Aceh Talks Raise Hopes for Settlement,” 23.
166

negotiators could enter new talks with hope that international concern for Aceh could 

be translated into a more evenhanded negotiation process.

Settlement in Helsinki

Talks reopened in Helsinki on January 27, 2005, just one month after the devastating 

tsunami. The Crisis Management Initiative (CMI), a Finland-based crisis-intervention 

NGO under the leadership of former Finnish President Martti Ahtisaari (1994 – 2000), 

served as the international mediator rather than the former Geneva-based Henry 

Dunant Center, although representatives of the latter organization were present to give 

advice. There were fi ve rounds of talks before a fi nal settlement was reached and 

offi cially signed on August 15, 2005.445

Offi cially titled a “Memorandum of Understanding between The Government of 

the Republic of Indonesia and The Free Aceh Movement,”446 the agreement became 

possible only after GAM, after thirty years of determined insistence, fi nally abandoned 

its demand for full independence and agreed to disarm. In return, the Government 

of Indonesia granted amnesty to all GAM fi ghters who laid down arms and agreed 

to implement a new law of autonomy for Aceh by March 31, 2006, in which a 

democratically elected government of Aceh would exercise authority in “all sectors 

of public affairs...except in the fi elds of foreign affairs, external defence, national 

security, monetary and fi scal matters, justice and freedom of religion, the policies of 

which belong to the Government of the Republic of Indonesia in conformity with the 

Constitution.” Aceh was “entitled to retain seventy (70) percent of the revenues from 

all current and future hydrocarbon deposits and other natural resources in the territory 

of Aceh as well as in the territorial sea surrounding Aceh,” and the government agreed 

to reduce its troop presence on Aceh to no more than 14,700 soldiers (from 35,000) 

and 9,100 police (from 14,000) by the end of 2005.

To supervise implementation of the agreement, the Memorandum of Understanding 

also established an Aceh Monitoring Mission (AMM) comprised of personnel 

contributed by the European Union and fi ve ASEAN nations. Although it was 

granted no coercive authority, both GAM and the Indonesian government committed 

themselves to accept the decisions of the Head of the AMM (Dutch diplomat Pieter 

Feith was the fi rst individual selected for this role447) and binding on them both.

445 All key documentation concerning the fi ve rounds of Helsinki talks, including the text of the fi nal 

settlement, is found on the CMI website, URL: http://www.cmi.fi . Accessed January 10, 2006. 

446 Text of the agreement at URL: http://www.cmi.fi /fi les/Aceh_MoU.pdf. Accessed January 10, 2006.

447 Associated Press, “Indonesia, Aceh Rebels Sign Peace Treaty,” The New York Times, August 15, 

2005.
167

Peace in Aceh at Last?

Although considerable skepticism remained on both sides, by the end of 2005 

implementation of the agreement was proceeding on schedule. The last of 840 arms 

required to be turned in by the GAM had been deposited with the AMM and destroyed 

by December 21, and on December 27, the Gerakan Aceh Merdaka formally dissolved 

itself. Indonesian troop movements out of Aceh also proceeded apace, with the fi nal 

3,353 troops boarding fi ve warships and a C-130 transport plane and departing the 

province on December 29. Much remained to be done to implement the political and 

economic phases of the agreement, but a further meeting in Helsinki between Vice 

President Kalla and former GAM leader Malik Mahmud (signer of the MOU for 

GAM) on January 21, 2006, continued to indicate positive progress on both sides.

On the darker side, both western and Acehnese observers took note of the arrival 

in Aceh soon after the December 2004 tsunami of several hundred Laskar Muhahadin

personnel and other Islamist groups-such as the Front Pembela Islam (FPI/Islamic 

Defenders Front)-many of whom had come on military transports.448 Ostensibly 

present to provide humanitarian relief like many other relief organizations arriving 

on the scene, they established command posts and set about distributing aid, burying 

the dead, and tending to the injured. Unlike their secretive presence in Maluku and 

Sulawesi three years earlier, they were now blatantly overt in Aceh, as Laskar Jihad

had been before. In the four command posts established by Laskar Mujahidin, signs 

were posted that read, “Islamic Law Enforcement.” Despite protests by western aid 

offi cials and also GAM leaders about the presence of these groups, Indonesian military 

offi cials generally defended their presence, arguing that their humanitarian support 

was needed and that they should not be discriminated against unfairly.449

GAM leader Malik Mahmud protested bitterly about the presence of these nonAcehnese militia groups. He argued that once GAM was disarmed these groups would 

be used to hunt down and kill former GAM members, since under terms of the amnesty 

government forces could not do this. He added, “If GAM defends itself against these 

militias, this will be the excuse the [military] is looking for to relaunch military 

operations.”450 Mahmud’s concern was undoubtedly well-founded. A key concern 

of Indonesian policy-makers throughout was the continuing suspicion that Acehnese 

nationalists perceived autonomy only as a fi rst step toward independence rather than 

the end of the process. Regarding this issue, the government and the Islamist groups 

were of one mind; Indonesia should remain a single, unifi ed state. The issue separating 

them was whether Pancasila or the shari`a should be the guiding ideology of the 

448 Zachary Abuza, “Out of the Woodworks: Islamic Militants in Aceh,” The Jamestown Foundation, 

January 28, 2005. URL: http://www.jamestown.org/news_details.php?news_id=88. Accessed November 

14, 2005.

449 Yang Razali Kassim, “GAM, Islam and the Future of Aceh,” IDDS Commentaries, February 8, 2005, 

1. Published in The Straits Times, February 12, 2005. URL: http://www.infi d.be/tsunami_gam_aceh. htm. 

Accessed December 23, 2005.

450 Associated Press, “Indonesia, Aceh Rebels Sign Peace Treaty,” The New York Times, August 5, 2005. 

URL: http://www.nytimes.com/aponline/international/AP.Aceh-Peace.html. Accessed August 15, 2005.
168

state. Regarding the role of the shari`a, on the other hand, the GAM and the Islamists 

were not at odds. In March 2002, following the adoption of the autonomy law by the 

Indonesian parliament in August 2001, the provincial government had been permitted 

to implement shari`a as the prevailing law of Aceh province.451 Through autonomy, 

therefore, Aceh held the potential for emerging as precisely that type of jemaah 

islamiyah Indonesian Islamists long had been seeking to create. Although, under the 

terms of the Helsinki settlement, some elements of the Indonesian government may 

have perceived a coincidence of interests between the government and the mujahidin

groups, they undoubtedly were also laying the groundwork for further confl ict in Aceh 

at some future date.

OUTLOOK

Eight years after the fall of the Suharto regime in 1998, the centrifugal forces 

unleased by the collapse of the strong, centralized, and dictatorial “new order” seem 

to have been largely contained. The anarchic politics of reformasi that followed 

opened the door to many possibilities. Aside from the loss of East Timor, the potential 

Yugoslavia-like breakup of Indonesia appears to have been averted, largely because 

of the adoption of reasonably liberal legal reforms permitting a higher degree of 

provincial autonomy and control of indigenous resources, plus the wealth derived 

from those resources in restive provinces like Aceh and Papua.

The terrorist threat posed by militant Islamist groups such as Darul Islam and 

Jemaah Islamiyah, although it continues, appears also to be in the process of being 

neutralized. Three major terrorist bombings after the Bali explosions in October 

2002 — of the J.W. Marriott Hotel in Jakarta in August 2003, the Australian Embassy 

in September 2005, and Bali again in October 2005 — communicate the continuing 

existence of fugitive elements, but the Indonesian dragnet launched after the fi rst Bali 

bombing also continues. The death in a police shoot-out in November 2005 of Dr. 

Azhari bin Husin, one of the men involved in all of the bombings, was yet another 

tightening of the noose around the militant movement, although Husin’s principal 

colleague, Noordin Mohamed Top, remains at large.

The violent character of the Islamist movements in Indonesia was at least in part a 

reaction to the violent methods of the Suharto regime in particular to suppress radical 

opposition to it. As the democratic institutions laid down in the original republican 

constitution seem fi nally to have begun to take root in the post-Suharto era, it can be 

expected that the views of those committed to the establishment of a shari`a-based 

political order can be more effectively articulated. Therefore the perceived need to 

retreat to violent action is likely reduced.

451 Human Rights Watch, “Asia, Indonesia,” Human Rights Watch World Report 2003, 5. URL: http://

www.hrw.org/wr2k3/asia7.html. Accessed December 5, 2005.
169

Thus far, Indonesian voters have rejected the Islamic alternative for the political 

organization of the state. The successful preservation of a democratic political process 

after years of dictatorial rule appears to be the central preoccupation of the Indonesian 

political establishment. To some degree, the fi rm Islamic opposition to Suharto’s rule, 

for which many paid a heavy price, can claim some credit for the ultimate demise of the 

regime and the reopening of the country to more democratic processes. The argument 

between those who champion Indonesia’s prevailing Pancasila ideology and those 

who seek change to a shari`a-centered political order has not ended, however. The 

struggle will likely divide Indonesia for the foreseeable future.
170

Map of the Philippines.

Source: CIA.
171

CHAPTER 6

ISLAM IN THE PHILIPPINES

If Filipinos will acknowledge the advantages of pluralism, if they will accept 

rather than reject it, then the various cultural groups can share a common 

loyalty to the national community while proudly retaining their distinctiveness.

 —Cesar Adib Majul

Despite relative Spanish success over a 300-year period at consolidating rule 

over the Philippine Islands, Christianizing the great majority of their population, and 

evoking by the late 19th century a growing sense of Filipino cultural identity among 

the disparate tribes and peoples that inhabited the archipelago, two areas that had 

continued to resist and elude fi rm Spanish control were the Igorot highland tribal 

people of northern Luzon and the Moros of Mindanao and the Sulu Archipelago in the 

southern region of the country. By 1898, when Spain was forced to transfer control 

of the Philippines to the United States as a result of losing the Spanish-American 

War, the sultanates of Maguindanao and Maranao on Mindanao, and Sulu in the Sulu 

Archipelago remained intact.452 From the standpoint of the sultans, they remained 

independent of Spanish control, although, of course, Spain claimed their territories as 

a part of its colonial holdings, as it had the territory of Sabah on Borneo until 1885, 

when in exchange for British recognition of Spanish control of Sulu it dropped its 

claims to Sabah.453

452 The predominately Tausug-inhabited Sulu archipelago had only one sultanate, based in Jolo. In 

Mindanao, two and sometimes three sultanates had existed among the predominately Maguindanao peoples 

that inhabited the Pulangi river valley that emptied into Ilana Bay on the west coast of the island. Further 

north, around Lake Lanao, the various tribes that constituted the Maranao people counted as many as 43 

sultanates (village states actually). In the Philippines, a sultan was a sovereign ruler who paid no tribute 

(taxes) to another. Subordinate rulers who paid such tribute to a sultan were called datus. Peter G. Gowing, 

Muslim Filipinos: Heritage and Horizon (Quezon City: New Day Publishers, 1979), 50.

453 Notably, although Spain may have dropped its claim to Sabah in 1885, the independent government 

of the Philippines after 1946 resurrected the issue, and it became a matter of fervent dispute between 

Malaysia and the Philippines in 1963, when Sabah was formally incorporated into Malaysia and again 

under the Marcos regime in the late 1960s. Not until after the fall of the Marcos regime did successor 

Philippine President Corazon Aquino attempt to rush a bill renouncing the Philippine claim to Sulu through 

the Philippine Congress in November 1987, just prior to a visit by Malaysian Prime Minister Mahathir 

Mohammad to attend an ASEAN summit in Manila. The Philippine Congress failed to act, however, leaving 

the issue technically unresolved. Ronald E. Dolan, Philippines: A Country Study (Washington, DC: U.S. 

Government Printing Offi ce, 1993), 237.
172

THE PHILIPPINES UNDER AMERICAN RULE

The Philippine Insurrection

Filipino independence leaders, headed by Emilio Aguinaldo, collaborated with 

the Americans during the brief war against the Spanish with the aim of achieving 

Philippine independence, issued a declaration of independence on June 12, 1898, and 

began forming an independent government in preparation for international recognition. 

Nevertheless, their hopes were betrayed by the Treaty of Paris, signed between Spain 

and the United States on December 10, 1898, in which the former colonial power ceded 

the Philippines, Guam, and Puerto Rico to the U.S. government, while granting Cuba 

its independence. The treaty provoked outrage throughout the Philippines and, as a 

result, U.S. occupation forces that grew to 76,000 soldiers before they fi nally prevailed 

in 1903 and found themselves engaged in major counterinsurgency operations aimed 

at preventing the U.S. from taking control of the country.454

Suspicious of both the Christian Filipino insurgents and the Americans, the Moro 

sultans did not join the insurrection, hoping to gain recognition as separate from the rest 

of the Philippines, while at the same time desiring American protection against Christian 

Filipino efforts to maintain the unity of the former Spanish colony. Accordingly, in August 

1898 the Sultan of Sulu, Jamal al-Kiram II, signed an agreement with U.S. General John 

C. Bates pledging Muslim neutrality in the U.S.-Philippines confl ict in return for a U.S. 

pledge of non-interference in the affairs of the Muslim populations of Mindanao and the 

Sulu archipelago.455

While U.S. military efforts to quell the Philippines independence movement 

continued, at the political level efforts were underway by a series of U.S.-led 

commissions to establish an American-guided governance structure for the whole 

of the Philippines that would “eventually” lead the Filipinos toward “self-rule.” The 

culmination of these efforts was the Philippine Organic Act of July 1902 that, with 

later changes, became the basis of the constitution governing the Philippines after its 

grant of independence by the United States in 1946. A part of this Organic Act was 

a division of the Philippines into provinces, one of which was a Moro province that 

encompassed both Mindanao and the Sulu archipelago.456

454 For a well-documented account of this struggle, see Stuart Creighton Miller, Benevolent Assimilation: 

The American Conquest of the Philippines, 1899 – 1903 (New Haven, CT: Yale University Press, 1982).

455 Gowing, Muslim Filipinos, 34.

456 The Philippines: A Country Study, 28 – 29.
173

The Moro Insurrection

Almost immediately, in 1903, efforts were 

begun to implement the provisions of the 

Organic Act. For the Moro province, like the 

others, these provisions meant an abolition 

of slavery; the establishment of new schools 

in which a new non-Muslim curriculum was 

provided; the construction of a new provincial 

government headed by a governor appointed 

from Manila, whose authority totally bypassed 

and undercut that of the historic sultans; 

and the traditional datus,

457 who viewed 

themselves as sovereign rulers and substituted 

a new legal system that replaced and totally 

ignored the shari`a. From the standpoint of the 

Moros, but especially their traditional datus, 

American policy in the Philippines was quickly 

perceived as more destructive and subversive 

to traditional culture than Spanish rule had ever 

been. Accordingly, U.S. authorities governing 

the Philippines soon found themselves faced 

with a second insurrection against their presence 

in the southern Philippines, one even more 

fi erce than the fi rst. The Moro insurrection that 

got underway just as the fi rst insurrection was 

being quelled continued until 1914, when U.S. 

forces fi nally were able to conclude that the 

457 The term datu, literally “ruler,” or “one entitled to rule,” is a complex term that generally refers to the 

leading male members and descendents of the ruling sultans’ families since the establishment of Islam in 

the Philippines in the mid-15th century. Referred to by one author as a myth of “sanctifi ed inequality,” the 

“myth” held that the men who fi rst brought Islam to the southern Philippines and became the fi rst sultans 

of Sulu and Mindanao were both of Arab origin and descendants of the Prophet Muhammad. According 

to the myth, only the descendants might carry the title of datu who formed a ruling class from which the 

sultans were drawn. The datus, therefore, constituted an aristocratic class, who were honored whether or 

not they held a formal position of leadership and authority. Thomas M. McKenna, Muslim Rulers and 

Rebels: Everyday Politics and Armed Separatism in the Southern Philippines (Berkeley, CA: University 

of California Press, 1998), 45 – 68. The term datu corresponds to the term tunku in Malaysia. Gowing, 48, 

notes that every datu was served by a pandita, a personal advisor in religious matters. The panditas and 

others, such as imams who had charge of mosques, constituted the Philippine `ulama class, but there was 

less sense of their acting as a collectivity in the traditional Philippines as in most Muslim countries. The 

datus more closely resembled the`ulama class found elsewhere in the Islamic world. McKenna later notes 

that it was only in the 1980s that the religious authority (but not necessarily the political authority) of the 

datus began to be successfully challenged by a new class of `ulama, the products of scholarship educations 

in Egypt and Saudi Arabia in the 1950s and 1960s and known locally as ustadz (teacher), who stressed the 

egalitarianism of Islam and the religion’s stress on social justice. McKenna, 200 – 207. It was around this 

new class of non-datu `ulama that the Moro Islamic Liberation Front (MILF) was formed by a minor datu, 

Salamat Hashim, in 1984. 

Photo of the Sultan of Sulu, Jamal al-Karim II, 

who signed an agreement with U.S. 

forces in 1898 pledging neutrality in the 

U.S. — Philippines confl ict in return for a U.S. 

the Muslim population of Mindanao and the 

Sulu archipelago.

Source: Peter G. Gowring, Muslim Filipinos: 

Heritage and Horizon (Quezon City: New Day 

Publishers, 1979). Used with permission.

pledge of non-interference in the affairs of 
174

major Muslim resistance groups had been subjugated and the Moro province could be 

released from military rule.458

Failure to Curry American Favor

American success in subduing the Moro insurrection led some Moro leaders to adopt 

a more positive attitude toward U.S. administrators of the Philippines. Whereas U.S. 

policy was formally aimed at achieving eventual Philippine independence, and U.S. 

administrators adopted a “policy of attraction” toward the ilustrado leadership class459

throughout the country, some Moro datus curried favor with the U.S. administration in 

the hope that through cooperation and goodwill they might eventually obtain support 

for a separate and independent Moro state. American policymakers, desirous of 

maintaining the goodwill of the large Christian majority in the Philippines, remained 

committed to the idea of Philippine unity, and in 1920 disestablished the American 

governor of the “Department of Mindanao and Sulu,” turning over responsibility 

for governance of the Moro region to the Bureau of Non-Christian Tribes of the 

recently established Philippine Department of Interior that reported to the Philippine 

Legislature (created in 1906). In response, a few months later, in June 1921, a group 

of 57 prominent datus in Sulu presented a petition both in Manila and Washington 

requesting that the United States either grant the Moros a separate independent state 

or retain their lands as “permanent American territory.”460

Later, in 1935, reacting to the U.S. decision to grant the Philippines Commonwealth 

status for a 10-year transition period prior to becoming independent, a group of 120 

Lanao datus (Mindanao) addressed a letter to President Franklin Roosevelt that read 

in part:

Because we have learned that the United States is going to give the Philippines 

independence, we want to tell you that the Philippines is populated by two different 

peoples with different religious practices and traditions. The Christian Filipinos 

occupy the islands of Luzon and the Visayas. The Moros (Muslims) predominate 

458 On the Moro insurrection, the major study is that of Samuel K. Tan, The Filipino Muslim Armed 

Struggle, 1900 – 1972 (Manila: Filipinas Foundation, 1977). For a brief account, see W.K. Che Man, Muslim 

Separatism: The Moros of Southern Philippines and the Malays of Southern Thailand (Quezon City: Ateneo 

de Manila University Press, 1990), 46 – 51.

459 The ilustrado or “oligarchy of intelligence” was a wealthy Filipino landowning, business, and 

professional elite that had emerged in the Christianized Philippines in the latter half of the 19th century, 

typically as a result of close collaboration with the Spanish colonial authorities. Often educated in European 

schools and universities, it was around this class that ideas of Philippine nationalism, as opposed to local 

ethnic identity, began to coalesce as well as among some, ideas of securing independence from Spanish 

rule. The Philippines: A Country Study, 16 – 22, 29. U.S. administrators cultivated this class during the 

colonial period, and its descendants have tended to dominate Philippine life until now. The Moro datu class 

were not technically a part of this class, but their role in the Moro areas was similar, and some responded 

by cooperating with American colonial rule and the independent Philippine state after 1946. For a detailed 

examination of this collaboration, see McKenna, Muslim Rulers and Rebels, 88 – 112.

460 Gowing, Muslim Filipinos, 168.
175

in the islands of Mindanao and Sulu. With regard to the forthcoming independence, 

we foresee what condition we and our children who shall come after us will be in. 

This condition will be characterized by unrest, suffering, and misery and because 

of this we do not desire to be independent. It is by living under the Stars and Stripes 

that those hardships would not bear down against us. The Americans have ever 

respected our religion, customs, traditions and practices. They have also recognized 

our rights to our property. The Americans have directed most of their efforts for the 

welfare of our people.461

Regardless of the relative accuracy 

of the prediction made in this letter, 

various U.S. administrations remained 

committed to maintaining the integrity 

of the Philippine state that had been 

ceded to the United States by Spain 

in 1898 and won by hard-fought 

battle.462 Most U.S. administrators, 

committed to a “civilizing mission” 

of promoting education, improved 

health care, economic development, 

rule by [American-derived] law and 

democratic principles of governance, 

and originating in a society that took 

religious tolerance and freedom of 

religion for granted, simply could not 

see that their well-intended efforts 

might fail to achieve the civilizing 

goal toward which they were 

directed, especially in “Moroland,” 

as they tended to call it. American 

administrators were also strongly 

infl uenced by the adamant opposition 

of Philippine Christian leaders, who 

represented 95 percent of the country’s 

population, to any diminution of the 

Philippine state. Moreover, although 

the largely Protestant orientation of most U.S. administrators led many of them to 

view the historically dominant role of the Catholic Church in the Philippines with 

461 Cited in Gowing, Muslim Filipinos, 169.

462 The ultimate rationale for this position was that failure to maintain the unity of the Philippine state 

might open the door to competing imperial powers — England, the Netherlands, Germany, Japan — to inherit 

parts of the Philippines left unclaimed by the United States. At the beginning, some, including Admiral 

Dewey, argued that the U.S. should lay claim only to Manila as an American naval base in the far Pacifi c 

and perhaps one or two other places as coaling stations. After the hard-fought battles to defeat the Philippine 

insurgency, however, it was politically diffi cult to challenge those who argued that the Philippines was 

America’s by right because of the blood and sacrifi ce expended by its soldiers and sailors during a more than 

decade-long military campaign. See Miller, Benevolent Assimilation, 13 – 30.

Map of the Philippines showing areas of Muslim 

concentration.

Source: Author.
176

some suspicion, their general view of the Moro lands, which they shared with most 

Christian Filipinos, was that they were inhabited by a backward and stubbornly 

unprogressive people who needed association with the more economically developed 

Christian-dominated Philippine state in order to share the benefi ts of the modern, more 

“civilized” world.463

During the period of direct American rule over the Philippines (until 1920 in the Moro 

province), American administrators did pay special attention to the Moro province. Its 

fi rst and only U.S. civilian governor, Frank Carpenter, was an educator who placed 

great emphasis on the building of schools and promoting universal education based on 

a modern [American-based] curriculum of instruction. The provision of health clinics, 

new roads and port facilities, telephone and telegraph networks and other infrastructure 

to promote economic development were also parts of the American program.

Christian Transmigration into Mindanao 

The establishment of a number of Christian Filipino agricultural settlements on 

the still sparsely populated island of Mindanao also had as its aim the more rapid 

economic development of the island as well as facilitating Christian-Muslim interaction 

and eventual integration of both as members of a united Philippine society. This last 

policy, which became a fl ood during the Commonwealth period (1935 – 1946) and 

continued unabated in the years after independence in 1946, became the primary 

issue that fi nally led to the emergence of the Moro separatist movement in the 1970s. 

The Moros were not pleased with all U.S. policies in their region, however, and were 

even less pleased when, in the years after 1920, administration of Moroland was 

increasingly in the hands of Christian Filipino rather than American administrators. 

Outbreaks of resistance were common, usually over specifi c issues and in specifi c 

locations, but were rapidly suppressed, at fi rst by U.S. forces, and later increasingly 

by elements of the Philippine Constabulary. The overall defeat of the Moros by U.S. 

forces by 1913 had gravely weakened them and prevented any immediate revival of 

a common struggle. Specifi c issues such as the cedula (a government-imposed head 

tax on all inhabitants) that the datus opposed because it eliminated their traditional 

role as revenue collectors; the requirement to turn in arms; opposition to compulsory 

education in the new government schools that did not teach shari`a; exactions for 

road construction; efforts to enforce monogamy; and maltreatment by the Philippine 

Constabulary464 were the usual sources of dissatisfaction.

463 Gowing, Muslim Filipinos, 38 – 42.

464 For details concerning many of the resistance movements, see Tan, Filipino Muslim Armed Struggle, 

32 – 42, and Che Man, Muslim Separatism, 51 – 56.
177

Table 3

Estimated Moro and Non-Moro Populations in Mindanao, 1903 – 1980

Moro Population Non-Moro Population

Year Number Percent Number Percent

1903 250,000 76 77,741 24

1913 324,816 63 193,882 37

1918 358,968 50 364,687 50

1939 755,189 34 1,489,232 66

1948 933,101 32 2,0101,223 68

1960 1,321,060 23 4,364,967 77

1970 1,669,708 21 6,294,224 79

1975 1,798,911 20 7,348,084 80

1980 2,504,332 23 8,400,911 77

Source: W.K. Che Man, Muslim Separatism: The Moros of Southern Philippines and the Malays of 

Southern Thailand (Quezon City: Ateneo de Manila University Press, 1990), 25. Citing Philippines, 

National Economic and Development Authority (1980a).

Transmigration: Source of Growing Alienation

By far the most irritating issue related to confl icts associated with land resettlement 

by Christian Filipinos on Mindanao. Historically, although there long had been small 

settlements of Christians on the island, they lived on lands claimed by the sultans

and paid taxes to them. The political authority of the sultans and datus was no longer 

recognized by the government created by U.S. administrators and was gradually 

turned over to Filipino administrators, having no clear title to most of these lands as 

new Filipino law required. Hence, it was not a diffi cult matter for Philippine offi cials 

to lay claim on behalf of the government to unsettled tracts of land for purposes of 

Christian settlement, particularly with the Philippine Constabulary available to enforce 

government policy. Matters became more critical during the Commonwealth period 

after 1935, when resettlement became part of an overall economic development plan 

for Mindanao (a reaction to the Great Depression of 1929). This plan, which foresaw 

aggressive settlement and economic development of Mindanao as a project benefi cial 

for the entire Philippine state and involved confi scation of settled lands for purposes of 

economic development, virtually ignored the original Muslim inhabitants of the land 

and was designed almost entirely around the new settlers whose numbers were growing 

rapidly. Signifi cant corruption in the National Land Settlement Administration (NLSA) 

that administered this plan also enabled a number of wealthy Christian speculators 
178

with advance knowledge of government plans to obtain title to lands that placed them 

in a position to exploit both Christian settlers and Muslim inhabitants of the island.465

Cooperation During World War II

Despite continuing and growing alienation between the Muslim inhabitants of 

the South and the emerging Philippine government, Moros generally joined in with 

Christian Filipinos and American forces in resisting the Japanese forces that occupied 

the Philippine islands between 1942 and 1945. Unlike their policy in Malaysia and 

Indonesia, where the Japanese had sought to empower the existing Malay Muslim 

national movements against the former colonial powers — Britain and Holland — they 

were equally harsh with both Muslims and Christians in the Philippines. Although a 

number of ilustrados and datus collaborated with the Japanese occupation forces in 

order to protect their private interests — a collaboration that became an important issue 

in Philippine politics after the war-a number of them also led resistance forces against 

the Japanese during the occupation.

The vast majority of Moros in fact were quite active in the resistance against the 

Japanese, as they had been against all forces trying to occupy their soil, be it the Spanish, 

the Americans, the Christian Filipinos, or the Japanese. Somewhat empowered by funds 

and large quantities of arms and ammunition provided by American submarines based 

in Australia, some Moros took advantage of the fall of the Commonwealth government 

to the Japanese to drive Christian settlers from their recently occupied farms into the 

cities of Mindanao, where the bulk of Japanese occupation forces were located. At the 

same time, they also collaborated closely with Christian Filipino resistance groups 

against the occupation.466

THE MOROS UNDER PHILIPPINE RULE

Early Benefi ts

The role played by the Moros during the war in resisting the Japanese produced 

several outcomes in the post-war period. In gratitude for their service, the restored 

Commonwealth government appointed a number of former Muslim guerrilla leaders 

(mostly datus) to high political offi ce (including governorships of the Moro provinces), 

and a number of Muslim leaders ran successfully for Congress. This policy continued 

under the independent Republican government after 1946, giving the Moros a sense of 

self-government they had not known for half a century.467

465 An excellent analysis of the settlement process is provided by McKenna, Muslim Rulers and Rebels, 

114 – 119. See also Cesar Adib Majul, The Contemporary Muslim Movement in the Philippines (Berkeley, 

CA: Mizan Press, 1985), 26 – 27, and Che Man, Muslim Separatism, 24 – 29.

466 Gowing, Muslim Filipinos, 181 – 182.

467 Majul, Contemporary Muslim Movement, 27 – 28.
179

Secondly, back pay awarded to those who could demonstrate their participation in 

the resistance and Japanese reparations payments to families for destroyed properties 

poured monies into the local economy, fueling a period of relative Moro prosperity. 

The impact of this new wealth cut two ways, however. On one hand, it tended to 

transform the Moro areas from a traditional barter economy into one based more on 

cash transactions, leading many to aspire to salaried jobs and professional and business 

careers, rather than traditional farming. As the economic bubble gradually receded by 

the late 1950s, however, the Moros increasingly became conscious of how relatively 

disadvantaged they were in relation to the rest of the country. On the other hand, the 

period of prosperity also facilitated a growing sense of Moro nationhood, a pride in 

being Moro that expressed itself in stronger commitment to Islamic activities. Hundreds 

now could afford to make the annual hajj (pilgrimage) to Mecca and began doing so. 

There was also an emphasis on the construction of new mosques and madrasas and a 

revival of numerous and often impressive, as well as costly, religious festivals.468

Finally, a third outcome stemmed from the large quantities of arms and ammunition 

that had come into Moro hands during the war. Determined not to be disarmed again, 

as they had been after the American suppression of the Moro resistance in the early 

part of the century, some Moros adamantly refused to turn in their weapons, while 

others simply proclaimed they had “lost” them. At least the Moros now possessed a 

stronger deterrent against government efforts to impose policies in the Moro areas 

they didn’t like.469

Acceleration of Transmigration

While the Moro region remained increasingly self-assured and relatively quiescent 

during the immediate post-war period, the major problem faced by the central 

government in Manila was the Hukbalahap (Huk) rebellion in central Luzon, the main 

northernmost island of the Philippines. Fundamentally a rural peasant uprising against 

rich landowners who dominated the Philippines both politically and economically, the 

movement was also a continuation of resistance against the Japanese occupation,470

with which so many of the wealthy landowners had collaborated. Although government 

forces ultimately prevailed by 1954, the Huk rebellion preoccupied the government 

for nearly a decade. One mechanism fi nally used by the government to defuse the 

rebellion was resettlement of some 950 families of former Huks on lands purchased 

for them by the government on Mindanao.471

468 Majul, Contemporary Muslim Movement, 28. McKenna, Muslim Rulers and Rebels, 136. 

469 Gowing, Muslim Filipinos, 183. 

470 The Hukbalahap, or People’s Anti-Japanese Army, had been organized in 1942 by Luis Taruc, a 

member of the Philippines communist party. An estimated 30,000 strong during the war, it was the leading 

resistance movement against the Japanese occupation in Luzon, but it was also opposed to any restoration 

of U.S. authority in the Philippines after the war, and also to the wealthy Filipino landowning class that 

exploited the peasants making up the Huk movement. Philippines: A Country Study, 41.

471 Philippines: A Country Study, 48.
180

The resettlement of the Huk rebels, who previously had held the status of criminal 

terrorists in the eyes of the government, and their families on Mindanao was only 

part of a much larger resettlement program that had resumed after the hiatus period 

of World War II. Now managed by the Army-administered Economic Development 

Corps (EDCOR), the program had as its goals not only relief of overpopulated areas in 

the northern Philippines by resettlement in the relatively underpopulated south but also 

the economic development of Mindanao as a means of more effectively integrating the 

southern islands into the Philippine economy. A part of this program was provision of 

low-interest loans and other forms of government assistance, such as new varieties of 

seeds, fertilizers, herbicides, tractors and farm machinery, as well as the building of 

new roads, irrigation networks, and swamp-draining projects. The recipients of the 

benefi ts of these programs were mainly the new settlers who happened to be Christian 

rather than the indigenous inhabitants who happened to be Muslims.472

The long-term result of these efforts was a major demographic shift in the population 

of Mindanao. Whereas in 1903 Muslims had constituted approximately 75 percent of 

the population of the island, by the 1960s they constituted no more than 25 percent, 

472 McKenna, Muslim Rulers and Rebels, 116 – 117.

Map of the southern portion of the Philippines, indicating predominantly Muslim areas of 

Mindanao, Sulu, and Palawan islands.

Source: HEAR Enterprise Company, San Juan, Metro Manila, Philippines. Provided to the author 

by Eugene Martin, United States Institute of Peace. Used with permission.
181

and signifi cant numbers of them had been driven off their farm lands and into villages 

or growing urban slums in the increasingly Christian major towns of Mindanao. More 

important perhaps than the demographic shift was the gradual “marginalization” of the 

Moros in their own lands, both economically and socially, if not entirely politically. 

In a purely technical sense, such marginalization need not have happened, for 

government policy offi cially provided equal access to state resources for both Christians 

and Muslims.473 The Moros, however, generally remained aloof from dealings with 

the government as much as possible, and they deeply resented offi cial efforts to forge 

Philippine unity by application of national laws that contradicted or did not take 

into account the requirements of Muslims under the shari`a. They also resented a 

nationally-run education program and curriculum designed to forge a strong sense 

of Philippine identity but that also seemingly designed to alienate their children 

from Islam.474 Then too, Philippine government administrators-mostly Christianidentifi ed more closely with the needs and aspirations of the settlers and tended to be 

oblivious to the needs and aspirations of the Moros, who preferred to minimize their 

contacts with Filipino administrators in any case. As the leading Muslim historian of 

the Philippines put it:

The increase of the non-Muslim population in [Mindanao] led many 

Muslims to conclude that there was a deliberate government scheme 

either to disperse them or to ensure that they remain a permanent 

minority in their own territories. They noted with frustration, if not 

envy, that the areas where the Christians had settled now had better 

roads and more effective irrigation projects, civic centers, and schools 

in comparison with their own backward facilities. So they believed that 

they were the victims of government discrimination and of neglect by 

their own leaders. In turn, Muslim leaders blamed all the ills on the socalled Christian government in Manila.475

Continued Moro Quiescence

Although perhaps it was only a matter of time before the situation reached some 

type of crisis, no organized opposition to the central government or its policies in 

the south emerged until the late 1960s and early 1970s. In part, this was due to the 

continuing role played by leading Muslim political fi gures as elected representatives to 

the Congress-often with the help of votes from Christian settlers who linked their own 

sense of security with voting for Muslim candidates-and the continued appointment of 

Muslim governors and mayors in Muslim majority areas. Usually these fi gures were 

members of the traditional datu class who had thrown in their lot with cooperation 

and collaboration with the central government, were still honored and remembered as 

473 McKenna, Muslim Rulers and Rebels, 118.

474 Majul, Contemporary Muslim Movement, 29 – 30.

475 Majul, Contemporary Muslim Movement, 32.
182

guerrilla leaders against the Japanese occupation, and continued to reap the benefi ts 

of participation in Philippine politics. Although the Moro population was in general 

alienated from the larger Filipino society, its members continued to respect their datus, 

a legacy of traditional Moro society that remained helpful in containing mounting 

Moro resentment.

Yet another mechanism used by the Philippine government as an effort to facilitate 

the integration of young Moros into mainstream society was education. In 1957, 

in response to a study of Moro needs, the government established a Committee on 

National Integration (CNI), the chief focus of which came to be the granting of 

scholarships to Muslims and other minority groups. Over the next 20 years, several 

thousand young Muslims were provided with free higher education at academic 

institutions in Manila, especially in law, which provided them entry into government 

and professional positions.476 Such educations, however, tended to promote cynicism 

about the old political order among the Moros, especially the datus and those political 

fi gures whom the students tended to defi ne as collaborators.477 Many became involved 

in a host of new activist organizations-the Muslim Association of the Philippines, the 

Muslim Progress Movement, the Agama Islam Society, the Sulu Islamic Congress, the 

Muslim Youth National Assembly, the Union of Islamic Forces, the Muslim Lawyers’ 

League, the Supreme Islamic Council, and others478 — that had as their aim the raising 

of Moro consciousness as Muslim Filipinos and advocating programs to benefi t their 

less fortunate countrymen. Although not originally intended as opposition groups, 

they did have the impact of giving voice to a new “articulately literate class” capable 

of analyzing and defi ning the plight of the Moros in new and more modern ways.479

Simultaneous with this trend was another set of scholarships that were made 

available during the same era for Muslim students from the Philippines to study in 

various universities in the Middle East. Several hundred Filipino Muslims studied in 

these years at universities in Egypt, Saudi Arabia, Syria, Algeria and Libya. Although 

some focused on professional studies, such as engineering or medicine, a great many 

devoted themselves to Islamic studies at Cairo’s al-Azhar University or the Islamic 

University of Medina, Saudi Arabia.480 The experience of these students had the impact 

of broadening their horizons and raising their consciousness of being connected to a 

larger Islamic world beyond their small provincial region in the southern Philippines. 

Many others also established contacts with fellow students from many parts of the 

Islamic world that later would be useful in soliciting international Islamic support for 

the Moros of the Philippines.

476 McKenna, Muslim Rulers and Rebels, 140.

477 Abuza, Militant Islam in Southeast Asia, 36.

478 Gowing, Muslim Filipinos, 186.

479 The term “articulately literate class” is that of McKenna, Muslim Rulers and Rebels, 136.

480 Che Man, Muslim Separatism, 57.
183

THE MORO REVOLT

The Moro National Liberation Front

The revolt, when it fi nally erupted in the early 1970s, was due to a variety of factors, 

in addition to those already mentioned. Centered on a new movement among the Moros, 

the Moro National Liberation Front (MNLF), the revolt was led by the new generation 

of university-educated Muslims from the south who conceptualized the Moros, not 

as Tausugs or Samals of Sulu, Maguindanao of Cotabato [Mindanao], Maranao or 

Iranun of Lannao [Mindanao], or Palawani or Molbog of Palawan, all owing loyalty 

to their respective datus or sultans, but as a single Muslim nation (Bangsa Moro), 

inherently separate from the rest of the Philippines, and more closely attached to the 

larger Islamic world of which the Moros were a part, especially the Malay Muslims of 

Indonesia and Malaysia.481

Established clandestinely in late 1968 or early 1969, the MNLF was a nationalist 

movement modeled after other anti-colonial resistance organizations that were 

common in many parts of the Third World in the 1960s, such as the FLN in Algeria, 

the PLO among the Palestinian Arabs, or the PULO among the Malays of nearby 

Thailand. Having as its aims the mobilization of general Moro support; the recruitment, 

training, and equipping of armed cadres to resist Philippine “imperialism”; and 

obtaining international backing for the justness of its cause, the MNLF unambiguously 

organized itself with the ultimate aim of achieving Moro political independence from 

the Philippines.

The Jabida Incident. The event that sparked the formation of the MNLF was the 

so-called Jabidah massacre of Muslim conscript soldiers on the island of Corregidor 

in Manila Bay in March 1968. President Ferdinand Marcos, elected President of the 

Philippine Republic in 1965, was widely perceived as engaging in a cover-up of the 

incident in order to dissociate his Presidency from it. Allegedly being trained for 

military operations in Sabah, a province of Malaysia since 1963, in support of the 

Philippines’ historic claim to that region, the Moro soldiers were said to have mutinied 

upon learning the purpose of their training and were killed in cold blood to ensure 

their silence. 

481 McKenna presents the interesting argument that the historic tendency of the Spanish, then the 

Americans, and fi nally the Filipinos themselves to conceptualize the Muslims of the southern Philippines as 

a more or less collective entity — the Moros — despite the vast ethnic diversity and inter — as well as intraethnic rivalries that characterized traditional “Moro” society and contributed to its weakness politically was 

fi nally absorbed by a critical mass of Moro students studying in Philippine schools and universities. In other 

words, the idea that the Moros constituted a single people was fundamentally a Western idea that was fi nally 

absorbed by those Filipino Muslims who had been drawn into the Philippine educational system with the 

purpose of facilitating their integration into Philippine society. The unintended consequence was to facilitate 

an idea of Moro nationalism, based on new and modern premises, that contributed to the formation of the 

MNLF. McKenna, Muslim Rulers and Rebels, 86 – 88, 110 – 112.
184

Although probably more rumor than fact-the government position was that the 

mutiny was over back pay issues and living conditions-the story was widely believed 

among the Moros and also in Malaysia, whose government lent its support to the 

newly established MNLF.482 The fi nal acquittal of those Philippine offi cers and 

soldiers associated with the killings sparked massive anti-government demonstrations 

in Manila and produced the resolve among many Moros to align themselves with the 

idea of an independent Bangsa Moro.

Christian Transmigrants React. Almost immediately, on May 1, 1968, Datu Udtog 

Matalam, the former infl uential governor of Cotabato [Mindanao], announced the 

formation of the Muslim Independence Movement (MIM) out of which the MNLF grew 

as its “student branch.” Its stated purpose was to “work toward gaining independence 

for Mindanao and Sulu.”483 Despite the apparent inactivity of the new organization, the 

growing popularity of the movement and of Datu Matalam caused concern among the 

Christian settlers of Mindanao, and various Christian militia groups began to emerge 

to defend Christian rights on the island. Although open confl ict did not emerge until 

1970, the atmosphere on Mindanao became increasingly tense, leading Datu Matalam 

at one point to change the name of his organization to the Mindanao Independence 

Movement (still MIM) in an effort to reassure Christian settlers, among whom the datu

had been historically popular.484

The MIM was in fact a cover organization for the MNLF, the student branch of 

MIM that was being organized clandestinely, primarily in Sabah, under the leadership 

of Nur Misuari, a former professor of politics at the University of the Philippines. What 

Datu Matalam and other datus associated with him did not realize at this point was that 

Misuari’s vision of the organization he was forming was that of a modern nationalist 

movement in which the traditional “feudalist” position of datu in Moro society would 

eventually have to be overturned. Confl ict between Misuari and the traditional datus

would in the end emerge as a source of grave weakness for the MNLF, when many 

datus turned back to collaboration with the Marcos government, as Misuari and the 

MNLF increasingly gained Islamic world recognition as the offi cial representative of 

the Moro cause in the southern Philippines. 

For the moment, however, the MNLF and the MIM worked in close collaboration. 

Key fi gures in the development of the MNLF were Matalam colleague Datu Rashid 

482 Che Man, Muslim Separatism, 139 – 140.

483 Majul, Contemporary Muslim Movement, 45.

484 McKenna argues that Datu Matalam, long a proponent of Christian-Muslim harmony in Mindanao, 

formed the MIM, not out of ideological reasons, but for personal political motives. A member of the 

Liberalista party, he was defeated in the 1967 elections for governor of Cotabato by a younger Muslim datu

who was aligned with President Marcos’ Nationalista Party. His personal interest, therefore, was less to 

achieve Moro political independence, despite his public stance, than to advance his own personal political 

standing among the Muslims of the Cotabato region. McKenna, Muslim Rulers and Rebels, 144 – 146.
185

Lucman of Lanao, Misuari, and Tun Mustafa, the elected governor of Sabah.485 In 1969 

a fi rst batch of 90 young Muslim recruits, mostly Maranaos provided by Lucman, but 

including Misuari, a Tausug from Sulu, quietly departed for Sabah to receive military 

training provided by professional Malaysian instructors under the overall guidance 

of Tun Mustafa. Additional groups were sent for training in the following years.486

On their return to the southern Philippines to train other recruits for the MNLF, they 

also smuggled in weapons provided by Tun Mustafa and the Malaysian government, 

and after 1972 by Libyan leader Muammar Qadhafi who became a major external 

supporter of the MNLF.

Outbreak of Violence. Growing sectarian tension in Mindanao erupted into violence 

in mid-1970. This was not a matter of Christian militias fi ghting Muslim militias, 

but rather of one militia attacking and burning the undefended village of the other 

sect and then being retaliated against by the destruction of a village associated with 

the offending militia — a strategy designed to infl ame tensions rather than to achieve 

victory. Such tit-for-tat violence continued through 1971, when by the end of the year 

it was estimated that more than 100,000 inhabitants of Mindanao from both sides had 

been made homeless refugees and 800 lives had been lost.487

Escalation of the Confl ict

Two events in 1971 and 1972 rapidly transformed the escalating confl ict into a fullscale civil war between the MNLF and the Government of the Philippines. The fi rst 

was congressional elections held in November 1971 in which Muslim candidates, for 

the fi rst time since the establishment of the Republic in 1946, were swept from offi ce. 

The growing insecurity in Mindanao led many Christians who previously had voted 

for Muslim candidates as a guarantee of their security now expressed their lack of 

confi dence in the Muslim datus by voting for Christian candidates. As a result, “political 

power in areas that historically had been part of the sultanates shifted from Muslims to 

Christians.”488 Some of the violence during 1971 had been politically motivated and 

designed to secure precisely the political results that occurred. Ironically, following 

the election, sectarian violence subsided and the security situation in Mindanao under 

the new political order became increasingly benign until the end of 1972, although the 

psychological shock of what had happened proved transformative.

485 Tun Mustafa was a Tausug Muslim with many close relatives living in Sulu and also a close associate 

of Datu Rashid Lucman. McKenna, Muslim Rulers and Rebels, 147 – 148.

486 Included in the second group in 1970 was Haj Ali Murad, later Chief of Military Operations of the 

Moro Islamic Liberation Front (MILF), a breakaway organization from the MNLF, and later head of the 

the MILF after the death of its founder and leader, Hashim Salamat, in July 2003. International Crisis 

Group, “Southern Philippines Backgrounder: Terrorism and the Peace Process” (Singapore/Brussels: ICG 

Asia Report No. 80, July 13, 2004),4. URL: http://www.crisisgroup.org/home/index.cfm?id=2863&l=1. 

Accessed April 13, 2005.

487 For a detailed analysis of this pattern of violence, see McKenna, Muslim Rulers and Rebels, 149 – 156. 

Also Majul, Contemporary Muslim Movement, 47 – 58, and Gowing, Muslim Filipinos, 192 – 196.

488 Majul, Contemporary Muslim Movement, 56.
186

Declaration of Martial Law

The second shock arrived on September 21, 1972, when 

President Ferdinand Marcos declared martial law throughout 

the Philippines. Although the communist-inspired New 

People’s Army (NPA), established in 1968, was a growing 

threat, it did not yet constitute the challenge to government 

authority posed by the Huk rebellion, its predecessor 

movement in the 1950s, and the proclamation of martial 

law only strengthened the appeal of the NPA within the 

country.489 The primary reason for Marcos’ action appears to 

have been to lay the basis for arresting and detaining about 

30,000 individuals whom he considered part of his political 

opposition, including rival politician Benigno Aquino.490 In 

publicly stating his rationale, however, he gave the principal 

reasons for the declaration of martial law the existence of 

armed confl ict between Muslims and Christians and a Muslim 

“secessionist movement” in the southern Philippines.491 From 

the perspective of the Moros, the declaration was the fi nal 

straw. It was a declaration of war against a defeated people who now had no option 

except that of resistance. 

Internationalization of the Moro Issue

Marcos may have been infl uenced in his decision to declare martial law by pressures 

coming from a number of Islamic countries expressing grave concern about the 

welfare of the Moros in southern Philippines. International reporting on the violence, 

especially with regard to those few cases where Philippine government forces seemed 

to be in league with the Christian militias, spurred charges of genocide and pressure 

on the Marcos government to be more active in preventing it. Malaysia and Kuwait 

were particularly vocal, but the most indignant was Libyan leader Muammar Qadhafi , 

who on October 7, 1971, made a bitter speech accusing the Philippine government of 

genocide. He also announced that he was sending a personal mission to the Philippines 

to study the situation and to provide aid to the refugees.492 Later, in January 1972, 

another delegation consisting of the ambassadors to the Philippines of eight different 

Islamic countries493 toured the south at the request of President Marcos to investigate 

489 Philippines: A Country Study, 280 – 290.

490 Philippines: A Country Study, 52.

491 Ferdinand Marcos, “Proclamation of Martial Law,” Philippine Sunday Express, 1, 141 (September 

24, 1972), 7.

492 Majul, Contemporary Islamic Movement, 55.

493 Egypt, Indonesia, Malaysia, Singapore, Pakistan, Iran, Iraq, and Saudi Arabia. Singapore, though 

technically not a Muslim country, nevertheless has a 15 percent Malay Muslim population, is a signifi cant 

regional entity, and is perforce closely tied to the affairs of its predominately Islamic region.

Ferdinand Marcos, 

controversial longtime President of the 

Philippines from 1965 

to 1986.

Source: URL: 

http://www.encarta.com.
187

the situation. Although their report absolved the government of charges of genocide, 

its description of the wretched plight of especially the Muslim refugees in Mindanao 

garnered widespread attention in the Islamic world.

The issue of the southern Philippines was raised at the Third Islamic Conference 

of Foreign Ministers (ICFM) that met in Jiddah, Saudi Arabia, between February 29 

and March 4, 1972. The Conference referred the issue to the Seventh Conference of 

the Research Academy of al-Azhar University (Egypt), scheduled to meet in Cairo on 

September 9, 1972. There on behalf of the Islamic Conference Organization (OIC) that 

would remain engaged with the situation in the southern Philippines until today, “the 

Conference passed a resolution expressing grave concern over the situation of Muslim 

Filipinos.”494 Two weeks later, despite the fact that violence in the south had virtually 

ended, at least for the moment, President Marcos made his decision to impose martial 

law, disestablish the Philippine Congress, and assume dictatorial authority.

Under the circumstances, “the imposition of martial law was, in fact the proximate 

cause, not the consequence, of [the] armed Muslim insurgency against the Philippine 

state,”495 that likely would at least have been delayed had there been no martial law. 

As it was, the Army moved immediately to collect all unauthorized weapons in the 

Philippines and a ban was placed on all political organizations. The moment was an 

existential one for the Moros of the Philippines. The choice was to submit or resist. 

Most Moros chose the course of resistance.

The MNLF Takes Charge

The ban on political organizations brought the clandestine MNLF to the forefront 

of the gathering confrontation. The previously above-ground organizations, such as 

the MIM or Salamat Hashim’s Nurul Islam, were immediately dissolved, with many 

of their members rallying to the MNLF. Salamat, later leader of the Moro Islamic 

Liberation Front (MILF) after his break with Misauri, became vice-chairman of 

the MNLF. Throughout the confl ict, the MNLF remained a loose-knit organization, 

which at best could only coordinate and support various groups of fi ghters operating 

independently in different sectors. The primary reason for its ascendancy derived in 

large part “from its access to critical resources, particularly weapons, from outside the 

Philippines.”496 These came primarily by boat from Sabah, having been delivered 

there from Libya and a number of other Muslim states.497

494 Majul, Contemporary Islamic Movement, 59.

495 McKenna, Muslim Rulers and Rebels, 156.

496 McKenna, Muslim Rulers and Rebels, 157.

497 Che Man, Muslim Separatism, 148.
188

Yet another reason for the MNLF ascendancy was the fact that it had gained the 

attention of the external Islamic world, which was a vital source of support for the 

Moro struggle. From fairly early in the confl ict, most of the top leadership of the 

MNLF, including Misuari and Hashim-wanted men in the Philippines-were in exile 

in Tripoli, Libya, where, with the support of Libyan leader Qadhafi , they constituted 

the “political front” of the MNLF, as opposed to its fi ghting arm in the Philippines, 

known as the Bangsa Moro Army. There, Datu Abulkhayr Alonto, a member of a 

prominent Maranao family in northern Mindanao, served as overall commander of 

military operations.

Civil War

Fighting erupted on October 24, 1972, the day before the deadline President Marcos 

had set for the turning in of all weapons. It quickly spread to most Muslim-populated 

areas of Mindanao and then Sulu, as Moro fi ghters, in accordance with an apparently 

well-coordinated plan, attacked government outposts and sought to take control of 

strategic positions vital for dominating the region. The government, somewhat 

surprised by the intensity of the uprising, sent thousands of troops south, and by late 

November fi erce clashes were taking place throughout the south between government 

forces and the Moro separatists.498

With the advantage of aircraft, helicopters, troop carriers, superior troop strength 

and mobility, as well as heavy weapons, the Philippine Armed Forces (AFP) were 

able to beat back most rebel attacks that were increasingly coordinated by the MNLF 

and to wreak devastating damage on towns and villages believed to harbor rebel 

fi ghters. Despite the advantages of the AFP, it could not end the rebellion, which only 

escalated over the next three years before fi nally abating in 1976. At its peak between 

1973 and 1975, the MNLF was estimated to be able to fi eld 30,000 fi ghters, while the 

Philippine military deployed 70 to 80 percent of its strength to contain the rebellion.499

The destruction caused in the Moro areas by both sides, but especially by the AFP, 

was massive. The war was estimated to have produced 50,000 deaths and a refugee 

population of over one million.500

Philippine government determination to crush the rebellion and to preempt the 

MNLF-led effort to establish an independent Bangsa Moro produced many outrages, 

such as the virtual destruction of the city of Jolo, the capital of Sulu and former seat of the 

498 McKenna, Muslim Rulers and Rebels, 156.

499 General Fortunato U. Abat, The Day We Nearly Lost Mindanao: The CEM-CON Story, 3rd ed. 

(Manila: FCA Publishers, 1999), 165 – 166.

500 Philippines: A Country Study, 291; Abuza, Militant Islam in Southeast Asia, 38.
189

Sultanate of Sulu, in February 1974.501 With each new report of even greater suffering 

of the Philippine Muslims, international Islamic world pressure, which previously had 

been exerted on the Marcos government to be more active in ameliorating the confl ict, 

now began to be exerted even more forcibly to achieve a diplomatic settlement. The 

Marcos government was highly subject to this pressure, because 40 percent of its oil 

imports came from these countries, especially Saudi Arabia and Iran, whose infl uence 

in international affairs after the 1974 oil crisis had been substantially augmented.502

International Intervention

The Islamic Conference Organization (OIC) and more particularly its Islamic 

Conference of Foreign Ministers (ICFM) were the principal agents for exerting this 

pressure. An important diffi culty was that the MNLF, whose leaders were perceived 

as wanted criminals by the Philippine government, was increasingly gaining the 

support of member countries of the OIC as the only representative with whom the 

Marcos regime could negotiate an end to the confl ict. Complicating this diffi culty 

was the demand of MNLF leader Nur Misauri that total Moro independence, which 

he was unable to win by force, was the only possible outcome of such a diplomatic 

settlement. For the Philippine government, much more able to effect its will on the 

ground militarily, the MNLF position was totally unacceptable, and no recognition of 

the MNLF was possible until it abandoned it.

501 On February 6, 1974, about 1,000 MNLF fi ghters attacked the Jolo airport and various army positions 

in the area of Jolo in an effort to retake control of the town. Government forces retaliated the following day, 

making use of tanks, aircraft and heavy offshore naval shelling, as well as a large number of ground troops. 

The city center was virtually destroyed before government forces could reclaim control over it several 

days later. The battle exacted heavy casualties on all sides, but especially among the civilian population 

of Jolo, while surviving MNLF fi ghters retreated and dispersed back into the countryside surrounding the 

town. Occurring just before a meeting of the OIC in Lahore, the Jolo “massacre” had a strong effect on the 

Conference delegates who supported a Conference resolution condemning the Philippine Army. Majul, 

Contemporary Muslim Movement, 66; Che Man, Muslim Separatism, 150. The Sulu archipelago emerged to 

be a critical theater of the Moro insurgency. Never as heavily impacted by Christian Filipino migration, its 

overwhelming Muslim majority (80 percent) was more strongly positioned to resist efforts of the government 

to maintain control. In addition, as a crossroads in the MNLF arms traffi cking program from Sabah, control 

of Sulu was of vital importance to both sides. The Tausug inhabitants of Sulu did little to diminish their 

historic reputation as the fi ercest warriors in the Philippines. Gowing, Muslim Filipinos, 188.

502 One important country that abstained from such interference was Suharto’s Indonesia, which never 

lent support to the MNLF and remained consistently as a voice within OIC councils recommending caution 

about intervening in the internal affairs of other states. Che Man, Muslim Separatism, 141 – 142.
190

The Tripoli Agreement

Negotiations between OIC representatives and Philippine government offi cials 

during 1973-74 proved tortuous and unproductive. A breakthrough was fi nally achieved 

when Marcos agreed to permit a Philippine delegation to meet representatives of 

the MNLF in Jiddah, Saudi Arabia, in January 1975. Such a meeting was possible, 

however, only after Misauri had agreed to negotiate on the basis of “autonomy” for the 

Moro areas instead of “independence.”503 Although the Philippine government did not 

at this time agree to the concept of autonomy, it nevertheless had fi nally recognized 

the MNLF as an interlocutor with whom it had to deal, and this step made further 

negotiations possible. Delaying tactics by Marcos and the glacial pace of the OIC 

deliberative process, however, meant that progress was slow, and it was not until 

December 23, 1976, that a fi nal “autonomy” agreement and general cease-fi re were 

reached between the government and MNLF representatives in Tripoli, Libya.504

Reaching an autonomy agreement was one thing; successfully implementing it was 

another. Continuing confl ict between the government and Muslim rebels since has been 

primarily over differences of interpretation of the Tripoli Agreement or perceptions of 

non-compliance by one party or the other. By the time the agreement was struck, the 

Marcos government had gained the upper hand over the MNLF, and the President 

appears to have been determined to implement its terms by fi at rather than by further 

negotiations between the two signing parties.

Weakening of the MNLF

In the years prior to the Tripoli Agreement, the MNLF, despite the continuing 

general support of the OIC, had found its position deteriorating. In 1974, due in 

part to a vigorous Philippine diplomatic campaign, the government of Malaysia 

offi cially changed its policy from support of Moro independence to that of supporting 

autonomy.505 Such a shift of policy made it diffi cult for Misuari to sustain the MNLF’s 

insistence that independence was the only solution for the Moro problem. Then, the 

electoral defeat in April 1976 of Sabah governor Tun Mustafa deprived the MNLF of 

the transit facility through which it had been able to maintain a supply of arms and 

503 Majul, Contemporary Muslim Movement, 68 – 69.

504 Text of the Tripoli Agreement is found in Majul, Contemporary Muslim Movement, 120 – 125. A 

major offshore earthquake and tsunami tidal wave that caused terrible destruction in western Mindanao 

in August 1976 brought a temporary end to the fi ghting, as Muslims, Christians, government troops and 

humanitarian organizations cooperated to bring assistance to the victims of the disaster. The occurrence 

of the tsunami may have contributed to the fi nally successful negotiations in Tripoli in December. The 

conjunction of events is eerily similar to the potential connection between the December 2004 tsunami off 

the coast of Sumatra and the August 2005 settlement between Aceh and Indonesia in Helsinki, Finland. 

Majul, Contemporary Muslim Movement, 72.

505 Abuza, Militant Islam in Southeast Asia, 38.
191

ammunition to the fi ghters in Moroland.506 The high civilian casualty rate also had a 

negative impact on popular support for the war, a trend Marcos sought to exploit by 

emphasizing the “communist” nature of the MNLF from whom all “good” Muslims 

ought to dissociate themselves. At the same time, he announced a general amnesty for 

rebel commanders who surrendered with their men, offering them cash or business 

incentives and positions in the government or the army if they did so. Many, especially 

those associated with datu families, did so.507 In July 1975, Marcos invited about two 

hundred former rebel leaders to a conference in Zamboanga that was billed as “peace 

talks” between the government and the “true voice” of the Moro people. Although 

this effort to discredit the MNLF did not succeed in altering OIC support for it and for 

Misuari’s leadership, it did highlight a deterioration of the organization’s authority, 

particularly in Mindanao.508

Meanwhile, even while pursuing a robust military campaign, President Marcos 

embarked on “a two-pronged campaign to convince Muslims in the Philippines and, 

more importantly, heads of Muslim states abroad, of his sincere desire to solve the 

“Moro problem.”509 On one hand, he inaugurated a major reconstruction campaign to 

rebuild the economic infrastructure in the south that was being destroyed by the war. 

Although most of the projects undertaken-airports, roads, and harbor improvementsactually served the needs of the military more than the general population of the region, 

the impression of commitment had a certain impact. On the other hand, he sought to 

demonstrate increased sensitivity to Islam by providing funds to build a large mosque 

in the center of Manila, permitting the establishment of an Islamic bank (Amanah 

Bank), establishing an Islamic Studies Institute at the University of the Philippines, 

offi cially recognizing Muslim holy days as government holidays, building statues and 

memorials to historic Moro cultural heroes, and encouraging the writing of a code of 

Muslim personal laws to be applied specifi cally for Muslims.510

Revival of the Traditional Sultans

A part of this strategy was to revive and reinvigorate the old datu system that the 

MNLF was seeking to undermine. In July 1974, a few months after the destruction 

of Jolo, Marcos formally recognized Datu Mahakutta Kiram as Sultan of Sulu.511

Although other members of the royal family contested this decision, the new sultan

506 Che Man, Muslim Separatism, 140.

507 McKenna, Muslim Rulers and Rebels, 167.

508 Majul, Contemporary Muslim Movement, 71.

509 McKenna, Muslim Rulers and Rebels, 166.

510 Cf. Majul, Contemporary Muslim Movement, 78 – 80.

511 When Sultan Jamal al-Kiram II, who had surrendered all claims to temporal authority to the United 

States (Gowing, Filipino Muslims, 50), fi nally died in 1936, the Commonwealth government declared that 

the offi ce ceased to exist. Although the inhabitants of Sulu failed to recognize this government decision and 

continued to choose one or several members of the royal family as rival claimants to the offi ce, the function 

remained only ceremonial and in fact continued to remain so after being revived by Marcos. Gowing, 

Filipino Muslims, 56.
192

was the man with whom the government would henceforth deal. About the same 

time, Marcos also gave formal recognition to fi fteen sultans among the Maranaos and 

three among the Magindanaons of Mindanao. Above them all he recognized former 

Congressman Rashid Lucman of Bayang as “Paramount Sultan of the Nineteen Royal 

Houses of Mindanao and Sulu.”512 Such was the reward to this datu cofounder with 

Nur Misuari of the MNLF, when he chose to break with the resistance and return to 

cooperation with the government.

The impact of all these actions was that by the time of the signing of the Tripoli 

Agreement in December 1976, the MNLF had been signifi cantly split and weakened. 

It remained primarily the continued support of external Islamic countries, embodied in 

the OIC, that enabled Misuari and the MNLF to remain a party to the agreement. But 

the agreement had a signifi cant benefi t to the MNLF leadership, in that they were no 

longer criminal elements in the eyes of the government and technically were able to 

return to the Philippines and play political roles in the new autonomous structure of the 

thirteen provinces identifi ed as having this status in the Tripoli Agreement.513

The MNLF was even further weakened as a result of the peace agreement with 

the government. If the threat of martial law and the perceived assault on the last 

vestiges of Moro independence was the great unifying factor enabling the MNLF 

as the dominant force leading the Moro revolt, peace proved to be an even greater 

threat to the continuing unity and solidarity of the organization. The split that emerged 

constituted basically a three-way break-(1) the original MNLF that remained loyal 

to Misuari, centered increasingly on his fellow Tausugs of Sulu, and largely led by 

secularly educated Muslims like himself with a fundamentally secular, nationalist 

agenda for the autonomous region defi ned by the Tripoli Agreement; (2) the MILF, 

a more religiously oriented organization, led (until 2003) by Salamat Hashim, 

formerly deputy leader of the MNLF until his break with Misuari in 1977, centered 

mainly on his fellow Maguindanaos of Cotabato and Maguindanao, and largely led 

by an emerging non-datu-connected `ulama class educated mainly abroad at various 

colleges and universities in the wider Islamic world; and (3) the BMLO (Bangsa Moro

Liberation Organization-later the MNLF-Reformed Group (RG)), headed at fi rst by 

Rashid Lucman, now “Paramount Sultan of the Nineteen Royal Houses of Mindanao 

and Sulu,” and led mainly by datus among the Maranaos of northern Mindanao, 

also Islamist in orientation, but more in tune with the traditional datu-dominated 

Islam of the past and positive about reconciliation with the government.514 The 

split represented geographical and regional as well as ideological differences within 

512 Gowing, Filipino Muslims, 56 – 57. See also Che Man, Muslim Separatism, 125.

513 Namely Lanao del Norte, Lanao del Sur, North Cotabato, South Cotabato, Maguindanao, Sultan 

Kudarat, Davao del Sur, Zamboanga del Norte, Zambuanga del Sur, Basilan, Sulu, Tawi Tawi, and Palawan. 

Majul, Contemporary Muslim Movement, 73.

514 Che Man, Muslim Separatism, 84 – 90. The author notes the existence of two other minor factions that 

split from the MNLF — the BMILO that stressed the need to spread Islam to all of the Philippines, but by 

dawa (proselytizing) rather than by violence; and the MORO, a Muslim revolutionary party associated with 

the Communist Party of the Philippines.
193

the MNLF and became apparent almost immediately after the cease-fi re mandated 

by the Tripoli Agreement that came into effect on January 20, 1977. When MNLFPhilippine government talks resumed in Tripoli in early March to refi ne the details 

of the Agreement, the BMLO, supported by Marcos, presented itself as the “true 

voice” of the MNLF. The OIC continued to recognize the leadership of Nur Misuari, 

however.515

Implementation of the Tripoli Agreement

The primary issue at stake in the follow-up talks in Tripoli was the defi nition 

of “autonomy.” The Tripoli Agreement had stated only that autonomy would be 

established in the thirteen provinces so designated. As he made clear in the second 

round of talks, Misauri’s vision of autonomy was the designation of the thirteen 

provinces as a single, autonomous region, presumably under the leadership of the 

MNLF. Government representatives resisted this demand, however, on the grounds that 

the Philippine Constitution required any such change to be subject to a local plebiscite 

in all thirteen provinces affected. There being a signifi cant majority of Christians in 

several of these provinces, and a slight majority of Christians in all of them combined, 

as well as clearly growing opposition to Misuari’s leadership of the MNLF, a number 

of the provinces would likely vote against unifi cation, and a single autonomous region 

would not come into being. Misauri, accordingly, opposed the idea of the plebiscite 

on the grounds that the Tripoli Agreement made no provision for it. The disagreement 

provoked an impasse that caused the talks to break down, never to be resumed until 

Corazon Aquino replaced Marcos as President in 1986. MNLF-sponsored insurgent 

activity soon resumed in the southern Philippines, although never again at the levels 

that the region had known between 1973 and 1975.

Despite the breakdown of the talks and the cease-fi re, Marcos pressed ahead with 

his own unilateral vision of autonomy. On March 25, 1977, he issued Proclamation 

Number 1628,516 in which he announced the formation of four regions into which the 

thirteen provinces were to be grouped.517 Although under martial law he perhaps did 

not need to do so, Marcos insisted that his proclamation be subject to a plebiscite in 

the thirteen provinces, which was held on April 17, 1977. The MNLF demand for a 

unifi ed autonomous province was included in the referendum. As expected, the MNLF 

program was rejected in favor of that expressed in the Presidential proclamation, and 

Marcos was able to assert that he had met the terms of the Tripoli Agreement.

515 Majul, Contemporary Muslim Movement, 85 – 90.

516 Text in Majul, Contemporary Muslim Movement, 126 – 128.

517 Region 4 (Palawan) Region 9 (Tawi Tawi, Sulu, Basilan, Zamboanga del Sur, Zamboanga del Norte) 

Region 11 (Davao del Sur, South Cotabato) Region 12 (Lanao del Norte, Lanao del Sur, Maguindanao, 

North Cotabato, Sultan Kudarat) Majul, Contemporary Muslim Movement, 127.
194

SPLIT IN THE MNLF

Emergence of the Moro Islamic Liberation Front

Misuari rejected this effort by Marcos to “dictate” the terms of autonomy in the 

Tripoli Agreement, called it instead a violation of the Agreement, and resumed his 

campaign for full Moro independence and secession.518 His intransigence, however, 

provoked an even deeper split with the MNLF, which became public and apparent 

later in the year at a meeting of the MNLF Central Committee in Mecca, Saudi Arabia, 

in December. There, his deputy, Salamat Hashim, arguing that Misuari was wrong to 

abandon the Tripoli Agreement and revive the campaign for independence, challenged 

his leadership of the MNLF. When the OIC and World Muslim League (Rabit alIslami al-Alami), meeting in Mecca at the same time, refused to accept his leadership 

challenge, Misuari expelled Hashim and 57 of his supporters from the organization. 

Hashim accordingly removed himself and his supporters from MNLF headquarters 

in Tripoli to Cairo and then later to Lahore, Pakistan.519 Salamat did not formally 

announce the formation of his rival Moro Islamic Liberation Front (MILF) until 1984. 

Nevertheless, the core of his new organization went with him, and his loss gravely 

weakened the MNLF, especially in the Cotabato region of western Mindanao.520

Rise of Salamat Hashim

Born in 1942 in Pagalungan, near Cotabato, Mindanao (Maguindanao Province), 

Salamat Hashim was to emerge, like many of those who followed his leadership, as 

a member of a new `ulama in the southern Philippines, trained and educated abroad. 

Although a minor datu himself, and related to some of Mindanao’s most distinguished 

Muslim political fi gures, he found on his return from Cairo in 1967 that these 

connections were of no personal use to him.521 Accordingly, he was drawn to the more 

radical separatist cause represented by the MNLF. A member of the fourth cohort of 

518 In October 1977, Misuari gave a blistering speech before the International Congress on Cultural 

Imperialism at the Palais des Nations in Algiers, in which he again accused the Philippine government of 

“cultural genocide” because of its brutal resistance to Moro efforts to achieve independence. Regardless 

of the merits of the analysis presented in the speech, it represents a profound articulation of the challenge 

faced by the Muslims of the Philippines to retain their identity as Muslims in the face of a non-Muslim 

government’s determination to control their cultural destiny. Full text of the speech in Majul, Contemporary 

Muslim Movement, 134 – 142.

519 Philippines: A Country Study, 292. Abuza, Militant Islam in Southeast Asia, 39. McKenna, Muslim 

Rulers and Rebels, 207. International Crisis Group, “Southern Philippines Backgrounder,” 4.

520 Even more serious was the defection in early 1980 of Salamat’s regional commander, Amelil Malaguoik 

(aka Commander Ronnie), with a number of his fi eld commanders to the government in exchange for being 

appointed the fi rst governor of the newly created autonomous region XII, which encompassed western 

Mindanao. Although this was a blow to the MNLF, it was a blow to Hashim as well, although he was able 

to slowly rebuild his position in the region, thanks largely to the loyalty and effectiveness of Commander 

Ronnie’s successor, Haj Ali Murad. McKenna, Muslim Rulers and Rebels, 208.

521 McKenna, Muslim Rulers and Rebels, 144.
195

Muslim students from Cotabato to receive scholarships to attend al-Azhar University, 

he departed for Cairo in 1959 and returned to the Philippines only after graduating in 

1967 to assume a minor position as a provincial librarian.

His years in Cairo coincided with those of certain Afghan students-Burhanuddin 

Rabbani, Gulbuddin Hekmatyar, and probably others-later to emerge as leaders of the 

Afghan resistance to the Soviet occupation of their country, who were also studying 

at al-Azhar at that time.522 Although no evidence exists to confi rm interaction 

during their student years in Cairo, Salamat’s decision to settle in Pakistan after 

his split with Misuari and his rapid involvement with the Afghan resistance suggests 

that his decision may have been infl uenced by going to a place where he knew he 

would be welcome.

A noted fi gure in any case as deputy leader of the MNLF to which he had rallied 

after the declaration of martial law by President Marcos in 1972, he, like most other 

leaders of the MNLF Central Committee, spent the years of the civil war residing in 

Tripoli, Libya, having personal recognizance over military operations in his native 

area of western Mindanao. A Philippine government document listing all ten meetings 

between various government representatives and the MNLF from June 1975 

to April 1979 demonstrates that Salamat was often the chief negotiator for the 

MNLF in lower-level meetings and was usually present when Misuari was leading 

the MNLF delegation.523

Hashim’s Islamic Vision

As the 1977 split between Salamat and Misuari made clear, however, the two had 

different visions on the role of the MNLF and how it should deal with the government. 

Whereas Misuari insisted on independence and the formation of a secular, nationalist 

state in which the traditional “feudal” datu order would have no place, Salamat, a 

religious scholar and a minor datu himself who nevertheless considered the datu

system antiquated, saw the movement more in religious terms. The quality that 

distinguished the Moros from other Filipinos was religious; they were Muslims, and 

other Filipinos were not. Whether Muslims achieved an independent state or only an 

autonomous region, where they were “free” to be Muslims, was not the point. What 

was necessary was for the Muslims of the southern Philippines to claim their rights as 

Muslims, and for this they required an Islamic political order that likely might be more 

possible under the autonomy agreement reached in Tripoli than under the political 

order envisioned by Misuari.

522 Olivier Roy, Islam and Resistance in Afghanistan (New York: Cambridge University Press, 1985), 

70.

523 Majul, Contemporary Muslim Movement, 143 – 144.
196

The Role of the Afghanistan Jihad

Salamat’s Islamic vision was strengthened and given greater clarity as a result of 

his experiences in Pakistan between 1982 and 1987. He quickly became involved 

with the Pakistani ISI’s (Inter-Service Intelligence Directorate) and Saudi-funded 

effort to recruit Muslims from around the world to assist the Afghan mujahidin in 

their struggle against the Soviet occupation of Afghanistan. Administered in large 

part by Usama bin Ladin, a son of the wealthy and powerfully connected bin Ladin 

family in Saudi Arabia, the program is said to have brought 35,000 potential fi ghters 

from different Muslim countries during the years 1982 –1992, 17,000 from Saudi 

Arabia alone.524 The Philippine contribution to this effort, organized and coordinated 

by Hashim Salamat, is estimated to have been 500-700.525 These generally arrived 

in small groups, either directly from the Philippines, generally Mindanao, where 

they had been recruited by Salamat’s local commanders, or indirectly from the large 

Filipino expatriate community living as workers abroad, especially in the Persian Gulf 

region.526 Among those who arrived in 1986 was Abdurajak Janjalani from Basilan, 

later head of the Abu Sayyaf terrorist group that became active in the Philippines in 

the 1990s. He reportedly had been engaged in studies in the Middle East, when he was 

drawn to participate in the jihad in Afghanistan.527

Unbeknownst to, or perhaps just not understood at the time by, Western supporters 

of the Afghan resistance, whose focus was on the U.S.-Soviet Cold War, Pakistani 

President Zia ul-Haq’s long-term policy for Afghanistan was to replace the Sovietsupported Communist government in Kabul with a regime that would constitute an 

“Islamic” government. For this reason, of the six resistance groups supported by the 

Pakistani ISI during the confl ict, only those three with clear Islamic political agendas 

received the bulk of Pakistani and U.S. support.528 Perhaps the Pakistani President 

was also engaged in a divide-and-rule strategy. For its part, Saudi Arabia preferred 

to distribute nearly all of its support through a group called Ittihad-i Islami (Islamic 

Union), headed by Abd al-Rasul Sayyaf, whose studies had been in Saudi Arabia, who 

spoke Arabic fl uently, and whose views on Islam closely paralleled those of the Saudi 

Wahhabi clerics among whom he had studied.529 Sayyaf, therefore, formed a seventh 

resistance faction supporting military resistance in Afghanistan, and it was primarily 

from his organization that the foreign fi ghters joining the resistance, including those 

524 Abuza, Militant Islam in Southeast Asia, 10.

525 Abuza, Militant Islam in Southeast Asia, 91.

526 International Crisis Group, “Southern Philippines Backgrounder,” 4.

527 Graham H. Turbiville, Jr., “Bearers of the Sword: Radical Islam, Philippines Insurgency, and Regional 

Stability,” Military Review (March – April 2002). URL: http://www.leavenworth.srmy.mil/milrev/ English/

MarApr02/turbiville.htm. Accessed June 6, 2005.

528 These groups were Gulbuddin Hekmatyar’s Hizb-i Islami, Burhanuddin Rabbani’s Jamiyat-i Islami, 

and Younes Khales’s faction of Hizb-i Islami. Supported, but at a much lower level, were Muhammad Nabi 

Muhammadi’s Harakat-e Inqelab Islami, Sibghatullah Mojadeddi’s Jebh-i Nejat-i Milli, and Pir Sayyid 

Gilani’s Mahaz-e Milli Islami. Roy, Islam and Resistance in Afghanistan, 119 – 121.

529 Roy, Islam and Resistance in Afghanistan, 123, 135 – 137, 212.
197

from the Philippines, received their training, lodging, and sustenance, primarily at 

Sayyaf’s mujahidin training school at Camp Saddah in Parachinar, Kurram Agency, 

Pakistan.530 For this reason, too, later Philippine terrorist leader Abdurazak Janjalani 

called his group Abu Sayyaf, after his former mentor in Afghanistan.

Establishment of the MILF

For Salamat Hashim, his role in Pakistan produced a new opportunity; he was now 

able to replace the MNLF training center in Sabah that had been closed in 1976, but now 

for the purpose of his own organization, the MILF, which he formally established in 

1984. Many of the Philippine fi ghters receiving training in Pakistan, such as Janjalani, 

stayed on to fi ght with the Afghan mujahidin. Others, however, fi ltered back home to 

join the resistance there and to become trainers for new recruits being raised locally. A 

feature of the 1976 Tripoli Agreement and cease-fi re had been the designation of several 

bivouac areas in remote locations as safe areas for MNLF fi ghters. In Mindanao, at 

least seven of these areas had been transformed into regular military camps — Camps 

Abu Bakar, Basrah, Ali, Omar, Khalid, Othman, and Salman-by 1985, now belonging 

to the MILF, under the leadership of Hashim’s local commander, Haj Ali Murad.531 To 

these camps the Filipino trainees returned, as did Hashim himself in 1987, following 

the fall of the Marcos government.

Another feature of the Pakistani experience for all those involved was association 

with Muslim resistance fi ghters from other parts of the Islamic world. In the case 

of Salamat and other MILF fi ghters, this meant not only a link with bin Ladin, but 

also compatriots from neighboring Indonesia, Malaysia, and Thailand. Much of the 

training at Sayyaf’s Camp Saddeh in Pakistan, the Filipinos learned, was carried out 

by Indonesians claiming to be part of the Darul Islam movement in their country.532

All these contacts would have later signifi cance when, after the formation of the 

Jemaah Islamiyah in 1992, al-Qa'ida training of MILF personnnel moved from 

Pakistan to Mindanao.

Continuing Resistance in Moroland

Although Moro resistance to Philippine government authority continued after the 

breakdown of the cease-fi re in 1977, it never again reached the levels of violence of 

the early 1970s, prior to the Tripoli Agreement. Sporadic attacks on Army posts or 

government facilities kept the Army on alert, periodically retaliating with massive 

dragnets aimed at capturing and/or killing wanted fugitives and/or terrorists, often 

with signifi cant “collateral damage.”533 The omnipresence of the Army in Muslim 

530 International Crisis Group, “Southern Philippines Backgrounder,” 14.

531 International Crisis Group, “Southern Philippines Backgrounder,” 5.

532 International Crisis Group, “Southern Philippines Backgrounder,” 14.

533 McKenna, Muslim Rulers and Rebels, 180 – 181.
198

areas made it clear that the new Autonomous Muslim Regions were still under 

military occupation. 

Nevertheless, Marcos persisted in implementing the autonomy scheme he had 

proclaimed and which had been approved by the plebiscite of April 1977. In January 

1981 the new Autonomous Regions were formally established; Muslims, mostly datus

and former MNLF commanders who had defected back to the government, were 

appointed to newly established regional government offi ces; and martial law was 

repealed, restoring constitutional government and paving the way for the restoration 

of electoral politics.534 The illusion of a cease-fi re was also maintained, for as long 

as MNLF/MILF fi ghters remained in their remote camps (MILF Liberated Zones, as 

they later came to be called), the government did not bother them; only outside of the 

camps did they become wanted fugitives and terrorists. 

The hollowness of the “autonomous” regional governments was apparent to all. 

They had no legislative or tax collection authority, nor any independent operating 

budget. All decisions continued to be made in Manila, and although the new regional 

governments soon employed a number of college-educated Muslims, the terror 

produced by the Philippine Army as it tried to master the continuing insurgency against 

its presence was the stark reality for most Filipino Muslims.535

In a letter to the OIC announcing his establishment of the MILF in 1984, Salamat 

Hashim noted that “The MILF operates as a parallel government vis-à-vis the enemy 

government within its area of responsibility and exercises infl uence extensively among 

the Bangsamoro masses in a degree more effective and binding than that of the enemy 

administration.”536 American anthropologist Thomas McKenna, in his fi eld research 

conducted in Mindanao in 1985 – 86, observed that such a “shadow government” did 

in fact exist in the particular areas that he studied. Although he noted that its impact 

was diffi cult to measure with any precision, his conclusion was that the MILF was 

more infl uential in most matters than the “enemy administration.”537

The MILF as the “Shadow Government” of Mindanao

A characteristic of the new “shadow government” gradually coming into being in 

the Cotabato area of Mindanao in the early 1980s, of which the MILF was to emerge 

as the symbolic authority, was the key role played by a new `ulama (called ustadzes538

in Mindanao) establishment that had not been apparent in earlier years. Most members 

534 Majul, Contemporary Muslim Movement, 99 – 100.

535 McKenna, Muslim Rulers and Rebels, 195.

536 Datu Michael O. Mastura, The Crisis in the MNLF Leadership and the Dilemma of the Muslim 

Autonomy Movement, Collected Papers of the Conference on the Tripoli Agreement: Problems and Prospects, 

September 13 – 14, 1985 (Manila: International Studies Institute, University of the Philippines, 1985), 18.

537 McKenna, Muslim Rulers and Rebels, 209.

538 In Arabic, ustadh — professor, teacher. 
199

of this new `ulama, like Salamat Hashim himself, were products of the scholarship 

educations many Mindanao Muslims had received in various Middle Eastern countries, 

particularly Egypt, beginning in the 1950s. As McKenna notes, however, “while their 

origins may be traced to the early 1950s, it is not accurate to speak of the ulama as 

a signifi cant religious force before 1980.”539 By 1980 their numbers appear to have 

reached a critical mass. The impact of the 1979 `ulama-led Islamic revolution in Iran 

had an inspirational impact, as did also the growing jihadist campaign against the 

Soviet occupation of Afghanistan, in which several hundred Muslim Filipinos would 

ultimately be engaged. Most importantly, however, the new ustadzes were increasingly 

supported by salaries paid by various Islamic world donors as part of the humanitarian 

assistance and reconstruction fi nancing provided to relieve the plight of the dispossessed 

and suffering Muslim refugees of the Philippines.540 Unlike the clandestine MILF, the 

new ustadzes were public fi gures who stressed the egalitarianian nature of Islam, the 

necessity of political leadership to represent the rights of the poor and oppressed, the 

need to live pure Islamic lives, and the importance of achieving Islamic unity in the 

face of the threats posed to their community. During the 1980s, the ustadzes rapidly 

emerged as a “counter-elite” that challenged the authority of the historic datus that 

were tending to collaborate with the “enemy administration,” and were infl uential in 

mobilizing popular support for the MILF.541

THE POST-MARCOS ERA

Fall of the Marcos Regime

The cronyism, corruption, high-handed authoritarianism, militarism, and brutality 

of the Marcos regime fi nally came to an abrupt end in February 1986, as a result of the 

popular People’s Power movement that garnered the support of millions of Filipinos to 

demand the ouster of the President and his replacement by Corazon Aquino. She was 

the widow of the assassinated Benigno Aquino, Marcos’ leading political opponent 

and critic who had strongly disagreed with Marcos about policy toward the southern 

Philippines. Beset by an even greater threat posed to the government by the communistinspired New People’s Army (NPA) that controlled large remote areas in the northern 

Philippines, the new President moved quickly in an effort to resolve the long-festering 

confl ict with the Philippine Moros.

The Jiddah Accord

In an unprecedented move, President Aquino in September 1986 paid an offi cial 

visit to MNLF leader Nur Misuari in his hometown of Maimbung on Sulu Island. 

There the two leaders agreed in principle to hold further talks that would result in 

539 McKenna, Muslim Rulers and Rebels, 205.

540 McKenna, Muslim Rulers and Rebels, 204 – 205.

541 McKenna, Muslim Rulers and Rebels, 213 – 214.
200

an end to hostilities, Aquino accepting Misuari’s demand for a single Autonomous 

Region rather than four, and Misuari accepting the government’s demand for autonomy 

rather than secession.542 Such an agreement was struck on January 4, 1987, in Jiddah, 

Saudi Arabia, during fi nal talks between Misuari and the Philippine government, 

represented by the President’s brother-in-law, Agapito Aquino.543 The promised unifi ed 

Autonomous Region would have its own elected governor and unicameral legislature 

and would have full control over its internal affairs, except for foreign affairs and 

national security.

Although the Jiddah Accord amounted to the fi rst diplomatic breakthrough since 

the Tripoli Accord of December 1976, it immediately ran into trouble on two counts. 

First, because it was negotiated only by Misuari as the sole spokesman of the Muslim 

peoples of the Philippines, the agreement was rejected by the MILF and was not well 

received by the traditional datu class that had been drawn into collaboration with the 

Marcos government. Within a week of its signing, MILF fi ghters on January 13, 1987, 

launched a series of attacks on government facilities and infrastructure in Cotabato 

City and other parts of southwestern Mindanao.544 Non-plused, Aquino immediately 

made plans to meet MILF military chief Haj Ali Murad in Cotabato City, which she 

did on January 18. Although the meeting resulted in a temporary cease-fi re, it did not 

result in MILF acceptance of Misuari’s leadership of the new Autonomous Region.

Secondly, the perceived softness of the new President toward the Moro rebels, as 

well as the NPA with whom she was also negotiating, added to her alleged general 

“incompetence,” led a number in the Army leadership that she had inherited from the 

Marcos era to attempt a coup d’état against her in late January 1987.545 Although the 

coup failed, as did subsequent rebellions culminating in the large and well-organized 

coup attempt in December 1989 that required U.S. air support to save the regime, 

the turmoil highlighted the weakness of her government and the chaotic politics that 

characterized the Philippines in the immediate post-Marcos period. Such weakness 

emboldened Moros still committed to independence rather than autonomy to reopen 

their struggle.

Return of Salamat Hashim to the Philippines

The new political situation in the Philippines led Salamat Hashim to return to 

Mindanao from Pakistan in 1987 along with a number of his Philippine Afghan 

veterans.546 Although Janjalani and a number of others are reported to have remained 

in Pakistan/Afghanistan until after the Soviet withdrawal from Afghanistan in February 

1989, Filipino support to the Afghan resistance basically ended in 1987, when Salamat 

542 McAmis, Malay Muslims, 98.

543 Philippines: A Country Study, 217.

544 McKenna, Muslim Rulers and Rebels, 246.

545 Philippines: A Country Study, 212.

546 International Crisis Group, “Southern Philippines Backgrounder,” 4.
201

decided that the changed political circumstances in the Philippines required his 

presence there. Upon his return, he established himself at Camp Abu Bakar, located 

in remote mountainous and jungle terrain north of Cotabato City, which was now 

MILF headquarters on Mindanao. Among his fi rst tasks was to establish in Camp Abu 

Bakar a military training “academy,” probably modeled on Sayyaf’s Camp Saddah 

in Pakistan, which was given the name Abdul-Rahman Badis Memorial Academy. 

Making use of his “Afghan alumni” to transmit the lessons they had learned on the 

Afghan frontier, a reported 122,000 MILF supporters received some sort of military 

training at Camp Abu Bakar, and a permanent force of some 10,000-15,000 armed 

regulars had been raised by 1990.547

Connections with al-Qa'ida

A role in supporting this effort fi nancially appears to have been played by Usama 

bin Ladin and perhaps also the government of Saudi Arabia.548 In 1988, bin Ladin 

had established his al-Qa'ida organization, and in the same year he dispatched 

his brother-in-law, Muhammad Jamal Khalifa, to Manila to take charge of the 

International Islamic Relief Organization (IIRO) offi ce there. The IIRO, a Saudi-based 

charitable organization, had been established in 1978 as a mechanism for providing 

humanitarian assistance to distressed Muslim populations, including those in the 

Philippines. Following the Soviet invasion of Afghanistan, it had been transformed 

into a major conduit for providing Saudi, U.S., and Gulf state funding to the mujahidin

in Afghanistan. 

Prior to being dispatched to Manila, Khalifa, a Lebanese Muslim, had from 1985 

to 1987 been director of the Muslim World League (Rabit al-Alam al-Islami) offi ce 

in Peshawar, where he no doubt had been active in cooperation with bin Ladin in 

coordinating the activities of the various Islamic world mujahidin that had descended 

on Pakistan. The IIRO offi ce in Manila was a regional offi ce with subordinate offi ces 

in Indonesia, Thailand, and Taiwan, as well as other subordinate offi ces in the southern 

Philippines.549 Although no specifi c evidence demonstrates that Khalifa’s IIRO was 

instrumental in helping to fi nance the growing strength of the MILF in the late 1980s, 

547 International Crisis Group, “Southern Philippines Backgrounder,” 4. Abdul-Rahman Ben Badis, for 

whom the Academy was named, was a notable leader of the Algerian `ulama during the 1930s who led a 

powerful movement opposing French control of Algeria, suggesting that Hashim perceived the situation of 

the Moros in the Philippines as analogous to that of the Algerians under the French.

548 It should be recalled that bin Ladin was not at this time the notorious fi gure he later became. In 1989, 

following the Soviet withdrawal from Afghanistan, bin Ladin returned home to a hero’s welcome in Saudi 

Arabia. It was only after Iraq’s invasion of Kuwait in August 1990 and the royal family’s decision to admit 

U.S. and other Western forces into the Kingdom to counter the Iraqi action that he broke with the regime 

and began his independent campaign to oppose Saudi rule and facilitate jihad against Western infl uence 

throughout the Islamic world. See Adam Robinson, Bin Ladin: Behind the Mask of the Terrorist (New 

York: Arcade Publishing, 2001), 123 – 130. Also Anonymous [Michael Scheuer], Through Our Enemies’ 

Eyes: Osama Bin Ladin, Radical Islam and the Future of America (Washington, DC: Brassey’s, Inc., 2002), 

112 – 115.

549 Abuza, Militant Islam in Southeast Asia, 92 – 93.
202

its subsequent role in underwriting the establishment and training of the Abu Sayyaf 

Group after 1992 suggests an earlier role in providing financial support to the 

MILF as well.

MILF Assumes Leadership of the Resistance

With the signing of the Jiddah Accord in January 1987, it was now Misuari’s MNLF, 

based in Sulu, that was working in collaboration with the government and Hashim’s 

MILF, based in Camp Abu Bakar, that had become the principal opposition. Despite 

the opposition, President Aquino, like Marcos before her, pressed on in implementing 

the Jiddah Accord as she understood it. On November 19, 1989, in accordance with the 

Philippine Constitution, voters in the thirteen provinces designated in the Tripoli Accord 

participated in another plebiscite to decide whether to join a new united Autonomous 

Region formally titled the “Autonomous Region of Muslim Mindanao” (ARMM). As 

Misuari had feared in 1977, but now accepted, only four provinces—Tawi Tawi, Sulu, 

Maguindanao, and Lanao del Sur—elected to join the new Region. Even Cotabato 

City, the pre-designated capital of the united Region, voted not to join, requiring the 

designation of another capital city instead.550 Nevertheless, President Aquino, moving 

forward to fully implement the Jiddah Accord, traveled south on November 6, 1990, 

to formally inaugurate the ARMM.

As sincere an effort as it may have been to create a fully autonomous ARMM, it 

left many problems unresolved. Many Muslims in the nine provinces that had voted 

not to join the ARMM, mainly because Christian voters carried the day, now found 

themselves vulnerable minorities in these provinces. The MILF camps were now both 

inside and outside the ARMM in relatively remote jungle locations. Left alone, beyond 

government control, they represented an even more autonomous, even independent, 

Muslim presence in the Philippines that seemed to mock the autonomy achieved 

in the four provinces of the ARMM. More Islamically-oriented than the secularlyoriented, MNLF-dominated ARMM, the MILF represented the continuing struggle of 

the Moros to achieve independence rather than the acquiescence of the MNLF. The 

continuing threat posed by the MILF, moreover, kept sizable numbers of the Philippine 

Army deployed in the south, especially Mindanao. Despite the Jiddah Accord and the 

ARMM, the Muslim areas of Mindanao in particular remained lands under military 

occupation, making something of a mockery of the concept of autonomy.

EMERGENCE OF ABU SAYYAF

As noted previously, sometime between April and December 1991, following his 

break with the Saudi royal family, Usama bin Ladin spent time in Pakistan/Afghanistan, 

where he recalled certain of his former associates to meet with him. Among those who 

joined him at this time included the Indonesians (though based in Malaysia) Abdullah 

550 Philippines: A Country Study, 211.
203

Sungkar, Abu Bakar Ba’asyir, and Hambali, who returned to Malaysia to establish the 

Jemaah Islamiyah organization in 1992/93. Yet another who came was the Filipino 

Muslim Abdurazak Janjalani. When Janjalani returned to the Philippines in late 1991, 

he was accompanied by Ramzi Yousef, who later would be involved as principal 

organizer of the fi rst World Trade Center bombing in New York in February 1993. 

Part of the agreement struck at this time was use of the MILF camps in Mindanao to 

train Jemaah Islamiyah recruits from southeast Asia, rather than to continue bringing 

them to the Pakistan/Afghanistan border area. For his part, bin Ladin appears to 

have agreed to provide fi nancial support and al-Qa'ida trainers. His brother-in-law, 

Muhammad Jamal Khalifa, and the IIRO, and perhaps other humanitarian assistance 

groups would serve as the conduit for fi nancial support. Ramzi Yousef and perhaps 

others accompanied Janjalani back to the Philippines to assist in training. Whether 

Salamat Hashim and Haj Ali Murad were party to this initial agreement or their 

cooperation was assumed is not certain. A fi nal part of the agreement seems to have 

been a commitment by Janjalani to establish an independent organization, the 

Abu Sayyaf Group, (ASG)551 which he began to do immediately upon his return 

to the Philippines.

Early Steps 

Janjalani’s home was Basilan Island, one of the nine provinces that had not voted 

to join the ARMM, and it was here, in a remote jungle area on Mount Kapayawan 

they called Camp Madina, that the ASG was established and headquartered. Other 

al-Qa'ida associates who joined Yousef at this time were Abdul-Hakim Murad and 

Wali Khan Amin Shah.552 Apparently with the concurrence of the MILF leadership, 

another camp for Abu Sayyaf recruits, Camp Shafi `ie, was established on Mindanao 

near the northern city of Marawi, which trained both ASG and MILF trainees in equal 

numbers-about 50 per year over a three-year period before 1995. Among those who 

matriculated through this program was Janjalani’s younger brother, Kadaffy Janjalani, 

who later replaced his elder brother as leader of the ASG after the former’s death in a 

shoot-out with police in 1998. Salamat’s cooperation with this program may have been 

due to its funding support being entirely from Khalifa’s IIRO.553

551 The Abu Sayyaf Group is an offshoot of another group, al-Harakat al-Islamiyah (The Islamic 

Movement), established on Basilan Island by a local Egyptian-trained (al-Azhar) ustadz, Wahab Akbar, in 

the late 1980s after Nur Misuari’s Jiddah Agreement with Philippine President Corazon Aquino. The two are 

often confl ated, and the distinction between the two is not clear. Fe B. Zaman, “Al Harakatul al-Islamiya: 

The Beginnings of Abu Sayyaf,” INQ7 Specials/Inside the Abu Sayyaf. URL: http://www.inq7.net/specials/

inside_abusayyaf/2001/features/formative_years.htm. Accessed September 3, 2005.

552 It was at this time that Yousef was given the nickname “The Chemist,” because of his knowledge and 

ability to construct a wide variety of bombs. Gunaratna, Inside al-Qaeda, 178.

553 International Crisis Group, “Southern Philippines Backgrounder,” 22.
204

Janjalani quickly announced the presence of the ASG by taking credit for two bomb 

attacks in Zamboanga City and Davao City in early 1992, also demonstrating that 

the new group’s scope of operations included the whole of Mindanao and not just 

Basilan Island.554 From these fi rst attacks until 1996, the ASG was credited with “67 

terrorist attacks, more than half of which were indiscriminant bombings. All led to the 

death of fi fty-eight people and 398 injuries.”555 Whereas MILF targets were typically 

Philippine Army outposts or government infrastructure facilities, what characterized 

the ASG attacks was that they generally aimed at the Christian presence on 

Basilan or Mindanao-either Christian symbols (e.g., churches), foreign or Filipino 

missionaries, or Christian towns, such as the southern Mindanaon town of Ipil, which 

the ASG attacked and burned on April 4, 1995, leaving 53 people dead and many 

others wounded.

Kidnapping for ransom also became an important method of operation of the ASG. 

Although demands for money later became a major motive for such kidnappings, it 

does not appear to have been necessarily so at fi rst. In April 1993, the ASG kidnapped 

a young fi ve-year-old Christian boy, Luis “Ton-Ton” Biel, on Basilan Island. The 

demands for his release included three requirements: (1) removal of all Catholic 

symbols in Muslim communities, (2) banning of all foreign fi shing vessels in the Sulu 

and Basilan seas, and (3) bringing the `ulama into the peace negotiation process with 

the Philippine government.556

Following the Biel kidnapping, the Philippine Armed Forces mounted a major 

operation to close down the ASG Camp Madina. They succeeded temporarily, but 

Janjalani and most of his followers managed to escape to Sulu Island, where they found 

refuge in jungle camps there. The fl ight to Sulu in fact resulted in a strengthening of the 

ASG, for the group soon was able to fi nd new recruits and to continue its operations 

without interruption.557

Abu Sayyaf Linked to Al-Qa'ida

The appearance of the ASG and the violence associated with it gravely compromised 

President Corazon Aquino’s efforts to implement the 1987 Jiddah Accord and the 

fully autonomous ARMM it had brought into being. After the settlement, the violence 

associated with the “Moro problem” was greater than before and was now characterized 

by pure acts of terrorism. At the time it was not clear if the ASG had an affi liation 

554 Many sources date the fi rst ASG attack as occurring in 1991, when a military checkpoint on Basilan 

Island was attacked by al-Harakat al-Islamiya supporters, led by Wahab Akbar, who subsequently fl ed to 

Malaysia. Zamora, “The Beginnings of Abu Sayyaf.” Although it may be an exercise in splitting hairs, 

this fi rst attack appears to have been a pre-ASG operation undertaken while Janjalani was in Pakistan/

Afghanistan meeting with bin Ladin.

555 Abuza, Militant Islam in Southeast Asia, 101.

556 Zamora, “The Beginnings of Abu Sayyaf.”

557 Zamora, “The Beginnings of Abu Sayyaf.”
205

with the MILF, was a secret arm of the MNLF, or was simply acting alone.558 What 

was known of Janjalani from those who had observed him was that “in his white 

fl owing robe, [he] was a vision of serenity [and] like a human magnet, attracting 

young Muslim scholars newly returned from studies in Saudi Arabia, Libya, Pakistan 

and Egypt, and local Muslims disillusioned with Misuari’s change of heart.”559 One 

affi liation became clear to Philippine authorities in December 1994, however, when 

after a bomb explosion on a Philippines Airline fl ight from Cebu to Tokyo, al-Qa'ida

operative Ramzi Yousef, the actual planter of the bomb, called the Associated Press in 

Manila and claimed responsibility for the explosion on behalf of the ASG.560

The subsequent arrest in early January 1995 of Yousef associate Abdul-Hakim 

Murad, in Manila, the discovery of Yousef’s laptop computer containing plans to 

blow up eleven U.S. airliners over the Pacifi c, and fi nally the arrest in February 1995 

of Yousef himself by authorities in Pakistan, led the Philippine government to draw 

a clear connection-for the fi rst time-between the ASG and bin Ladin’s emerging alQa'ida organization. Although it probably was not directly connected with the alQa'ida conspiracy in Manila known as Operation Bojinka, the alleged association of 

the ASG with an act of international terrorism forced Philippine government authorities 

to begin thinking about it in an entirely different light.

RAMOS AND THE MORO PROBLEM

Retired General Fidel Ramos had replaced Corazon Aquino as President of the 

Philippines in June 1992, and it was he who faced the new challenge seemingly 

posed by the ASG. Throughout the years of martial law until the overthrow of Marcos 

(1972-1986), Ramos, a graduate of the U.S. Military Academy at West Point, had been 

chief of the Philippine Constabulary, the bureau of the government having primary 

responsibility for law and order throughout the country, including the south. Long 

a Marcos loyalist, he switched sides to join the People’s Power movement in 1986, 

bringing signifi cant military support with him. Upon Ramos assuming the Presidency, 

a grateful Aquino appointed him Chief of Staff of the Armed Forces during the fi rst 

two years of her six-year term, and then Secretary of National Defense during her fi nal 

558 There later even arose suspicions that the ASG may have been a clandestine Philippine Army 

operation aimed at discrediting the Moro insurgency. In February 1995, Ibrahim Yakub, one of the original 

ASG cadre of 30, “came in from the cold,” and it was subsequently learned that his real name was Edwin 

Angeles and he had been working as a government agent within the ASG. As operations offi cer for the 

ASG, he had been in charge of every ASG operation, including the Biel kidnapping, the concept for which 

was said to have originated with him. After his return to government service, he continued to assist by 

identifying his former ASG colleagues as they were caught by government authorities. In January 1999, he 

was assassinated outside a mosque in Basilan. Whether the ASG or Philippine government services were 

behind the assassination is not clear. Where his true loyalties lay was also unclear. “Edwin Angeles: The 

Spy Who Came in from the Cold,” INQ7 Exclusive. URL: http://www.inq7.net/specials/inside_abusayyaf/ 

2001/features/spy-turns-bandit.htm. Accessed September 3, 2005.

559 Zamora, “The Beginnings of Abu Sayyaf.”

560 Simon Reeve, The New Jackals: Ramzi Yousef, Osama bin Ladin and the Future of Terrorism (Boston: 

Northeastern University Press, 1999), 80.
206

four years in offi ce. Now the twelfth President of the Philippine Republic and with 

great experience with the long Moro rebellion, Ramos sought to move decisively to 

reach a fi nal resolution of the problem of the Moro south.561

Animated, like most Filipino leaders, by the view that economic deprivation was 

the primary factor underlying Moro dissatisfaction rather than cultural uniqueness and 

a strong sense on the part of the Moros, although articulated many times, that they 

were not Filipinos, Ramos placed great stress on economic development programs and 

a policy of reaching a formal peace agreement between his government and that of the 

ARMM. In 1993, strongly supported by the governments of Malaysia and Indonesia, 

he opened talks with MNLF leader Nur Misuari, who was still recognized by the OIC 

as the offi cial representative of the Bangsamoro people, despite the fact that the fi rst 

elected governor of the ARMM had been Linding Pangandangan. Gradually, Jakarta 

emerged as the principal venue for continuing talks and the site of the fi nal agreement 

reached between the Ramos government and the MNLF on August 30, 1996. 

The Jakarta Agreement

Formally called the “Final Agreement on the Implementation of the 1976 Tripoli 

Agreement between the Government of the Republic of the Philippines and the Moro 

National Liberation Front with the Participation of the Organization of the Islamic 

Conference Ministerial Committee of Six and the Secretary-General of the Organization 

of the Islamic Conference,” or more simply the “Jakarta Agreement,” it was offi cially 

signed by President Ramos and MNLF leader Misuari in the Malacanang Presidential 

Palace in Manila on September 2, 1996.562

Among other things, although the 1989 plebiscite had resulted in the grouping 

of only four Muslim provinces into the ARMM, the new Agreement recognized 14 

provinces (13 plus a newly created province of Saranggani) and nine cities as part 

of the Autonomous Region. Although another plebiscite would have to be held to 

confi rm this part of the Agreement, such language was not part of the Agreement, and 

Ramos made no effort to hold one during the course of his administration. Another 

provision of the Agreement was for MNLF fi ghters to be integrated into the Philippine 

Constabulary and the Armed Forces, with primary responsibility for enforcing law 

and order in the ARMM.563 Within a week of signing the Agreement, on September 

9, 1996, new elections resulted in Nur Misuari, with the full backing of the Ramos 

administration, being chosen as the new governor of the ARMM as well as Chairman 

of a newly formed Southern Philippines Council for Peace and Development (SPCPD) 

561 Data on Ramos drawn largely from “President Fidel Ramos,” Neofi noy.Info. URL: http://www. 

neofi noy.info/The%20RP%20Presidents/ramos.htm. Accessed September 5, 2005.

562 McAmis, Malay Muslims, 99.

563 As a result of the Jakarta Agreement, 5,070 MNLF fi ghters laid down their arms, and 2,200 were 

integrated into the Philippine Army or police. Others, however, rallied to the MILF or ASG or simply 

remained outlaws. Abuza, Militant Islam in Southeast Asia, 42. 
207

that was also created by the Jakarta Agreement. Yet another provision of the Agreement 

was the establishment of an Offi ce of Muslim Affairs, a central Philippine government 

agency tasked with assessing and responding to the needs of the Philippine 

Muslim community.

Misuari Again in Charge

Under the terms of the Jakarta Agreement, and following his election as Governor 

of the ARMM, Nur Misuari assumed the role of principal peace broker in the southern 

Philippines on behalf of the government, with primary responsibility for dealing with 

and neutralizing the continuing opposition of the MILF and the ASG. With funds made 

available to him as Chairman of the SPCPD and still maintaining signifi cant moral 

authority over MNLF fi ghters being integrated into the Army and police, Misuari 

fi nally was being vested with signifi cant powers to resolve the long-festering 

problem of the southern Philippines. The only price was acceptance of autonomy 

rather than independence for the Bangsamoro people, which Misuari now seemed 

committed to doing. 

For President Ramos, the linchpin of his policy was the SPCPD, through which 

he proposed to channel much needed government funds to promote the economic 

development especially of the resource-rich, but war-ravaged, island of Mindanao.564

Moreover, through the Jakarta Agreement, he had gained OIC promises of support for 

the economic development of the ARMM, Malaysia and Indonesia being especially 

enthusiastic to play a positive role in promoting investments in the region. 

During the Ramos years, at least until the Asian fi nancial crisis that hit all of 

southeast Asia in July 1997, the Philippine economy that had languished during the 

latter Marcos years and remained hostage to the political instability that marked the 

years of the Aquino administration fi nally began to experience the “Asian miracle” of 

rapid economic growth that characterized the entire southeast Asian region during the 

1980s and 1990s until the 1997 collapse. In part, this was due to the President’s own 

strong hand in implementing reforms designed to open up the once closed national 

economy, to encourage private investment, and to reduce corruption.565 Moreover, 

this economic growth was being felt in the south. Although per capita income in the 

southern Philippines was estimated to be only two-thirds of that in the rest of the 

country, it was growing at a more rapid rate than elsewhere in the country during the 

Ramos years.566

564 For a listing of proposed economic projects for the ARMM after the Jakarta Agreement, see the 

ARMM website. URL: http://park.org/Philippines/government/armm.htm. Accessed September 5, 2005.

565 “President Fidel Ramos.”

566 See “The Autonomous Region in Mindanao.” URL: http://www.mindanao.org/mindanao/overview/

muslim1.htm. Accessed September 5, 2005.
208

General Success of the Ramos Policy

The Ramos policy and the Jakarta Agreement did have a positive short-term 

impact on conditions in the south, as MILF- and ASG-sponsored violence diminished 

signifi cantly over the next several years.567 Possibly the uncovering of the al-Qa'ida

Operation Bojinka plot in early 1995 led Filipino militants associated with the 

perpetrators to lay low for a period of time. An absence of violent resistance did not 

mean acceptance of the provisions of the Jakarta Agreement by either the MILF or Abu 

Sayyaf, however. In late 1996, Salamat Hashim convened a Bangsamoro Consultative 

Assembly at Camp Abu Bakar in which 200,000 people from throughout Mindanao 

were reported to have attended. There, the Assembly strongly expressed its opposition 

to the Jakarta Agreement, calling instead for an independent state.568

Cease-fi re with the MILF

Undaunted, the Ramos administration pressed its agenda of low-profi le meetings 

with MILF representatives in provincial towns around Mindanao, fi nally reaching 

a 3-year cease-fi re agreement between the government and the MILF on July 18, 

1997.569 A part of this agreement was government acceptance of the various MILF 

camps in Mindanao, or “liberated zones,” as Hashim preferred to call them, as secure 

areas that the Army would not attack if not provoked. Ramos’ clear strategy was to 

buy time for economic development projects to improve the living conditions of 

the inhabitants of the region, which he believed was a precondition to a peaceful 

settlement. Accordingly, “in addition to projects in the ARMM, the government 

began to implant other projects in MILF-held territories, including the Narcisso 

Ramos Highway linking Cotabato to Marawi, including a 15-km road to the MILF 

headquarters at Camp Abu Bakar; a water system for 10,000 people; an irrigation 

system for 2,500 people; and the Malmar Dam.”570

The “Shadow Government” Emerges

The new circumstances seemed to embolden Salamat Hashim’s confi dence. “In 

December 1997, the MILF held its 15th general assembly, and was so assured of his 

hold [on its territories] that the assembly was all but public knowledge.” And Salamat 

closed the assembly by holding a public press conference for the fi rst time.571 “Like 

all unjust, oppressive and corrupt governments,” he said, “the Manila government will 

collapse...when this happens, the Bangsamoro Islamic government will automatically 

567 Larry Niksch, Abu Sayyaf: Target of Philippines — U.S. Anti-Terrorism Cooperation, CRS Report for 

Congress RL31265 (Washington, DC: Congressional Research Service, January 25, 2002), 3.

568 Rigoberto Tiglio, “Moro Reprise,” Far Eastern Economic Review, December 26, 1996.

569 International Crisis Group, “Southern Philippines Backgrounder,” 6.

570 Abuza, Militant Islam in Southeast Asia, 45.

571 Abuza, Militant Islam in Southeast Asia, 45.
209

arise.”572 His confi dence was perhaps based on the idea that, under the terms of the 

cease- fi re, he was in fact operating a government in the “liberated zones” under his 

control as a virtually independent state, certainly more independent than the ARMM. 

And in his view, it was an Islamic government, operated and supported by the

`ulama throughout Mindanao, and governed by the shari`a administered by Islamic 

courts.573 The authority of the MILF’s “shadow government” in the rest of Mindanao 

also engendered confi dence. Time, in his view, was on the side of the MILF, not the 

Philippine government.

Connections Between MILF and al-Qa'ida

Hashim’s confi dence was also no doubt bolstered by the secret relationship that was 

emerging between the MILF and bin Ladin’s al-Qa'ida organization. In 1994, after 

having agreed a year earlier to establish Camp Shafi `i for the training of Abu Sayyaf 

and his own MILF fi ghters, he made an agreement to host a new Jemaah Islamiyah

training facility at Camp Hudaibayah, a remote location within the larger Camp Abu 

Bakar. To supervise this effort, al-Qa'ida leader Abu Zubayda in October of that year 

appointed from Afghanistan Omar al-Farouk whom, with several other al-Qa'ida and 

Jemaah Islamiyah operatives, he sent to the Philippines to establish and oversee the 

new camp.574 Funded by al-Qa’ida, the primary mission of Camp Hudaibiyah was “to 

conduct jihadist training” for Jemaah Islamiyah recruits, primarily Indonesians, of 

whom more than one thousand were reported to have received training in Mindanao 

during the years 1996-98.575 Initially, the al-Qa'ida trainers appear to have been 

mainly Arabs from camps in Afghanistan, but soon Indonesians were very involved 

in the training as well. Maintaining the security of this clandestine Jemaah Islamiyah

training may well have been a key reason behind Hashim’s acceptance of the new 

cease-fi re.

From the Jemaah Islamiyah perspective, the Philippines was part of Mantiqi 

3, which included all of Borneo (including the Malaysian provinces of Sabah and 

Sarawak, as well as independent Brunei) and the eastern Indonesian island of Sulawesi. 

The mission of Mantiqi 3 was almost purely training, whereas the mission of Mantiqi 

1 (peninsular Malaysia, southern Thailand, and Singapore) was primarily to serve as 

a headquarters, transit point, banking center, and safe haven for planning. In general, 

military operations in these regions were avoided in order to maintain the security of 

the primary mission. The primary long-term target of Jemaah Islamiyah operations 

572 Cited in Maria A. Ressa, Seeds of Terror: An Eyewitness Account of al-Qaeda’s Newest Center of 

Operations in Southeast Asia (New York: Free Press, 2003), 128.

573 Further details in Ressa, Seeds of Terror, 128, and Abuza, Militant Islam in Southeast Asia, 45, 

136 – 137.

574 Ressa, Seeds of Terror, 134. The fi rst trainees that virtually built the new Camp Hudaibiyah were 

MILF recruits who used machetes to clear the jungle for the camp that was said to be up and running by 

April 1995, the same month the ASG attacked and destroyed the Christian town of Ipil. International Crisis 

Group, “Southern Philippines Backgrounder,” 14.

575 Ressa, Seeds of Terror, xv.
210

was clearly Mantiqi 2, the main islands of Indonesia. Although from the beginning 

Jemaah Islamiyah had a pan-Malay perspective and envisioned the eventual unity of 

all the Malay Muslim areas of Southeast Asia under a single Islamic government, the 

destabilization and eventual capture of Indonesia was clearly the short-term goal of 

Jemaah Islamiyah operations. The Jemaah Islamiyah leadership was Indonesian, as 

were most of its foot soldiers. The opportunity to launch such operations came only 

with the fall of the Suharto government in Indonesia in May 1998. In the meantime, its 

foot soldiers prepared, primarily in the MILF camps.

From the al’Qa'ida perspective, support for the Jemaah Islamiyah was part of 

its overall global strategy after the Soviet withdrawal from Afghanistan to support 

militant Islamist movements throughout the Islamic world that were striving to put 

an end to the generally authoritarian secular regimes, most often supported by the 

Western powers, and especially the United States, which had come to dominate 

most Islamic states during the 20th century. A second aspect of al-Qa'ida strategy, 

at least at the beginning, appears to have been to make use of the linkages that 

had been created as a means of gaining access to the Philippines as a base from 

which to conduct global operations, particularly against the United States. The 

failed Operation Bojinka, directed by Ramzi Yousef and uncovered by Philippine 

authorities in January 1995, was evidence of this intent, but the failure appears 

to have ended al-Qa'ida efforts to make use of the Philippines for this purpose, 

at least temporarily.

That al-Qa'ida and the MILF did not always share the same objectives was 

demonstrated on October 14, 1997, when two Arab trainers from Camp HudaibiyahMuhammad Gharib Ibrahim Sayid Ahmad and Ragab al-Makki-conducted a suicide 

attack on a Philippine Army headquarters near Cotabato, killing six. Clearly designed 

to disrupt the 3-year cease-fi re that had been signed between the MILF and the 

government of the Philippines in July, it failed to achieve its end, as President Ramos 

and Salamat Hisham both interpreted the action for what it was and agreed to maintain 

the peace. Although Abuza interpreted this event as an effort to bolster the morale of 

MILF fi ghters who had been disillusioned by Hashim’s agreement to the cease-fi re, 

a more likely interpretation is that al-Qa'ida disapproved of the cease-fi re agreement 

and sought to disrupt it.

Following the bombing of the U.S. embassies in East Africa in August 1998, 

the al-Qa'ida training centers in the Philippines and elsewhere assumed increased 

importance, as U.S. and Pakistani authorities intensifi ed efforts to make it more 

diffi cult for al-Qa'ida recruits to use Pakistan as a transit point for individuals to reach 

the training camps in Afghanistan. Accordingly, Salamat Hashim acceded to requests 

from the al-Qa'ida leadership to open two more camps in the MILF areas that came 

to be called Camps Vietnam and Palestine, to be used exclusively by Arab and other 

Middle Eastern personnel.576

576 Ressa, Seeds of Terror, 7, 133.
211

How much Philippine authorities knew about the clandestine training occurring in 

MILF camps in Mindanao at this time is unclear. Most information about it emerged 

from later interrogations of arrested individuals after the resumption of fi ghting in 

2000. While Ramos remained President, both he and Salamat exerted strong efforts 

to maintain the cease-fi re and to overlook isolated incidents that could have led to a 

resumption of fi ghting. Despite the cease-fi re with the MILF, the government had no 

such agreement with the Abu Sayyaf Group, however, and on December 18, 1998, early 

in the term of Ramos’s successor, President Joseph Estrada, Philippine constabulary 

forces managed to locate and kill ASG founder Abdurazak Janjalani in a shootout in 

Lamitan on Basilan Island.577

Impact of the Death of Janjalani

The death of Janjalani had the impact of splintering the ASG into at least fi ve groups, 

each claiming to be the real ASG, but in fact operating more or less independently. 

Of these, two major factions were those commanded by the founder’s brother, 

Khaddafi Janjalani, on Basilan Island and by Galib Andang, alias Commander Robot, 

operating in the Sulu Archipelago.578 If the Philippine government believed it had 

resolved the problem of Abu Sayyaf by eliminating Janjalani, events soon proved it 

sadly mistaken. At best, Janjalani had played an important role in maintaining the 

ASG’s cohesion, strategy, and tactics. With his death as a martyr to those who had 

followed him, the successor Abu Sayyaf groups emerged as not only vengeful, but 

more vicious and terrifying.579

A revived ASG, now headed by Khaddafi Janjalani, was heard from again when, 

on March 20, 2000, his group kidnapped more than 50 people from two elementary 

schools on Basilan Island, including a number of school children. Calling for release 

of three al-Qa'ida-linked prisoners held in United States prisons in exchange for the 

hostages, the incident clearly implied an international dimension that transcended the 

local Moro struggle in the Philippines. Although most of the school children were 

soon released in return for food and medicine, the kidnapping crisis went on for 44 

days before the last hostages were released. In the meantime, the ASG kidnappers had 

murdered several of the hostages, including two by beheading, and others were killed 

by government forces while securing their release by force.580

577 Turbiville, “Bearers of the Sword,” 6.

578 Ressa, Seeds of Terror, 109.

579 Eusaquito P. Manalo, “The Philippine Response to Terrorism: The Abu Sayyaf Groups,” unpublished 

master’s degree thesis (Monterey, CA: Naval Postgraduate School, December 2004), 35 – 36.

580 Ressa, Seeds of Terror, 109 – 110. The three al-Qa'ida-linked prisoners in the United States were the 

Egyptian Shaykh Omar Abd al-Rahman, imprisoned because of his alleged role in the February 1993 World 

Trade Center bombing, Ramzi Yousef, and Abu Haidal (Mir Aimal Kasi), imprisoned because of his role in 

killing two and wounding three CIA employees in northern Virginia in January 1993.
212

Not to be outdone, on April 23, 2000, Commander Robot’s group of Abu Sayyaf 

in the Sulu Archipelago crossed over to Sipidan Island off the coast of Sabah in 

Malaysia and kidnapped 21 tourists from seven countries whom they brought back 

to Sulu as hostages. Although the kidnappers lectured the hostages about the ASG’s 

struggle for an independent Islamic state, in the end all that was demanded for their 

release was $20 million – $1 million for each hostage — which was duly delivered in 

September by the government of Libya, allegedly under pressure from the affected 

European governments which were said to have reimbursed Libya for at least part of 

the ransom.581

In the early stages of the crisis, ARMM governor Nur Misuari, who had access to 

the Abu Sayyaf kidnappers, was tasked by the Estrada government with resolving the 

crisis. On May 8, however, he was replaced by the former Libyan ambassador to the 

Philippines, Rajab Azzarouk, who in 1996 had played an important role in facilitating 

the Jakarta Agreement between the Philippine government and the MNLF. European 

Union emissary Javier Solana also arrived in the Philippines to play a role.582 The end 

result was the $20 million ransom that fi nally secured the release of the hostages on 

September 9, 2000.

The $20 million made the ASG incredibly rich. For a time, its contribution to the 

local economy far exceeded any government program, and recruits fl ocked to join 

the Abu Sayyaf Group. CNN journalist Marie Ressa argues that media interest in the 

kidnapping, which led journalists to pay handsome sums for guides and transportation 

and the right to interview individual hostages, not to mention the king’s ransom at the 

end, transformed ASG terrorist operations into a virtual money-making industry that 

had benefi ts for many throughout the Philippine government, including perhaps even 

President Estrada himself. Some speculated that as much as half of the $20 million 

went back to al-Qa'ida.

583

581 Ressa, Seeds of Terror, 112 – 116. The kidnapped hostages were from Finland (2), Germany (3), 

France (2), South Africa (2), Lebanon (1), Malaysia (7), and the Philippines (2). One of the Filipinos was 

never released and was believed to have joined the ASG.

582 AIJAC (The Australia/Israel and Jewish Affairs Council), “Asia Watch,” in The Review, website of 

the AIJAC. URL: http://www.aijac.org.au/review/2000/256/aw256.html. Accessed September 13, 2005.

583 Ressa, Seeds of Terror, 115.
213

THE DIFFERENT APPROACH OF JOSEPH ESTRADA

Although these Abu Sayyaf operations took place far from MILF areas of control, 

and MILF leaders distanced their organization from these terrorist operations, even 

issuing fatwas condemning kidnapping and the beheading of kidnapped hostages, the 

violence of the ASG provoked communal tensions throughout Mindanao. With the 

three-year cease-fi re between the government and the MILF up for renewal in the 

summer of 2000, the increased tensions had both the Army and MILF fi ghters on high 

alert. A ferry bombing off Ozamis City in northern Mindanao on February 25, 2000, 

which killed 39 passengers, by terrorists whom the Army claimed had taken refuge 

in MILF Camp John Mack in Inudaran, Lanao del Norte, led to a military stand-off. 

Denying the presence of the perpetrators, the MILF camp found itself attacked by 

Philippine Armed Forces on March 17, just three days before the Abu Sayyaf attack on 

the two elementary schools on Basilan Island. Camp John Mack commander Abdullah 

Macaapar (Commander Bravo) responded by sending forces out of the camp to attack 

and occupy the nearby town of Kanswagan, a move that led to full-scale fi ghting 

between the two contending forces.584

President Joseph Estrada, elected to replace former President Fidel Ramos in June 

1998, scorned his predecessor’s policies of “coddling” the Muslims of the southern 

Philippines,585 although he took no overt steps to undermine the cease-fi re with the 

MILF until it came up for renewal in 2000. A former popular movie actor-turnedpolitician who was soon to be constitutionally impeached and driven from offi ce in 

January 2001 because of alleged massive corruption, Estrada believed the Philippine 

Army should defeat the MILF rather than coexist with it. Accordingly, on April 27, 

four days after the ASG Sipidan Island kidnapping, he declared an “all-out war” 

against the MILF and the ASG.586

Estrada Takes the Offensive

Although fi ghting was general throughout the south over the next several months, 

with many former MNLF fi ghters again taking up arms and joining the MILF, 

and upwards of 900,000 civilian refugees being created by the general violence, a 

particular strategic target was the 15-km road connecting Camp Abu Bakar with the 

main Cotabato-Marawi highway that recently had been constructed by the Ramos 

administration. Heavily fortifi ed and guarded by the MILF, the road ultimately could 

not be defended, and Philippine Armed Forces succeeded in breaking through to Camp 

Abu Bakar on July 9, taking control of MILF headquarters.587 The MILF leadership, 

including Salamat Hashim, escaped, however, to the more remote Jemaah Islamiyahcontrolled Camp Hudaibiyah, which continued to hold out against government forces 

584 International Crisis Group, “Southern Philippines Backgrounder,” 6.

585 Abuza, Militant Islam in Southeast Asia, 46.

586 International Crisis Group, “Southern Philippines Backgrounder,” 27.

587 International Crisis Group, “Southern Philippines Backgrounder,” 6.
214

until April 2001. Unknown publicly at this time, the Indonesian Jemaah Islamiyah

cadres training in Camp Hudaibiyah began vacating the camp and returning, mainly 

to Indonesia, to establish new camps there that within a year were receiving MILF 

recruits for training.588

MILF Reactions

Anticipating the outbreak of hostilities with the Philippine government, the 

MILF in 1999 had begun establishing a Special Operations Group (SOG) under the 

leadership of Afghan war veteran Mukhlis Yunos.589 In doing so, Yunos worked closely 

with Indonesian Jemaah Islamiyah fi gures, the most notable of which was another 

Afghan war veteran and explosives expert, Fathur Roman al-Ghozi.590 In April 2000, 

Salamat Hashim had responded to President Estrada’s declaration of “all-out war” 

against the MILF (the independent Bangsamoro Islamic state, as Hashim preferred 

to conceptualize it) by labeling the emerging struggle as a jihad against the would-be 

occupiers of the MILF “liberated zones.” Very quickly, on May 3, 2000, Yunos’ SOG 

responded by setting off four bombs in General Santos City that killed three. This 

attack was followed by another bomb at the SM Megamall in Manila on May 21 that 

killed one, and six more bombs in General Santos City on June 24 that killed two.591

These clearly terrorist operations against civilian targets marked a departure for the 

MILF that heretofore had adhered closely to conventional guerilla tactics of attacking 

military targets and government facilities within the Muslim-inhabited areas of the 

Philippines. They did not deter government operations, however, which continued on 

until the capture of Camp Abu Bakar on June 9.

The fall of Camp Abu Bakar and most other MILF camps produced a lull in the 

fi ghting, not because the Philippine Army had achieved victory, but because the MILF 

needed time to undertake a major reorganization, decentralizing what had become a 

quite centralized military force592 and making it more capable of conducting guerrilla 

operations. That MILF retaliation against Philippine “aggression” would have a 

different dimension, however, became apparent on August 1, 2000, when a bomb 

exploded outside the residence of the Philippine ambassador to Indonesia, Leonides 

Caday, in Jakarta, seriously wounding the ambassador and killing two bystanders. 

Although not known until after his capture in Manila on January 15, 2002, this 

operation was carried out by Indonesian Jemaah Islamiyah operator Fathur Roman 

al-Ghozi and others, as a kind of “thank-you note,” so some said, to the MILF for the 

training and assistance provided to the Jemaah Islamiyah in recent years.593

588 Ressa, Seeds of Terror, 139.

589 Abuza, Militant Islam in Southeast Asia, 98.

590 Ressa, Seeds of Terror, 136.

591 International Crisis Group, “Southern Philippines Backgrounder,” 11, 27.

592 International Crisis Group, “Southern Philippines Backgrounder,” 10, provides some detailed 

information about this reorganization.

593 Abuza, Militant Islam in Southeast Asia, 97 – 98. For details, see International Crisis Group. “Southern 

Philippines Backgrounder,” 18.
215

The major act of retaliation for the fall of Camp Abu Bakar was to come in Manila 

on Rizal Day, December 30, 2000, when the MILF SOG carried out fi ve simultaneous 

bombings, striking a train, a bus, the airport, a park near the U.S. Embassy, and a gas 

station, killing 22 people and injuring more than 100. A dramatic event, Philippine 

authorities at this time had no idea that the bombings had an Indonesian connection.594

Again, unrealized until after the capture of al-Ghozi and also Mukhlis Yunos on May 

25, 2003, the bombings were an MILF SOG operation in which al-Ghozi had been a 

principal advisor. Jemaah Islamiyah leader Hambali had come to Manila a few days 

earlier to examine the plan and give it his seal of approval, as well as funds ($3,600) 

to Yunos to pay for his expenses.595 The confusion over the Rizal Day bombings was 

only complicated by the occurrence six days earlier, on Christmas Eve, of 30 nearly 

simultaneous bomb blasts in Christian churches across Indonesia, also orchestrated by 

Hanbali, which killed 19 and injured about 120 people.596

The Impeachment of Joseph Estrada

The year 2000 had not been a good year for the Philippines and, in January 2001, 

President Joseph Estrada faced impeachment proceedings on grounds of massive 

corruption while in offi ce, including widely believed allegations that he had derived 

profi t from the $20 million ransom paid in September by the Libyan government 

to the ASG for release of the Sipidan hostages. Never formerly found guilty by the 

Philippine Senate, Estrada nevertheless was forced to step down from offi ce only after 

the Supreme Court had declared the Presidency vacant and swore in his Vice President, 

Gloria Macapagal-Arroyo, as his constitutional successor on January 20. Claiming 

that he never had been formally removed from offi ce nor resigned, Estrada and his 

supporters continued to challenge the legitimacy of the Arroyo government in legal 

disputes likely to keep Philippine politics in turmoil for the foreseeable future.597

ARROYO RESTORES THE RAMOS POLICY

Formerly Vice President in the Estrada administration, Arroyo, the daughter of 

former Philippine President Diosdado Macapagal (1961-65) and a former professor 

of economics, was elected in her own right as President in June 2001. Meanwhile, 

she inherited the problems of the Estrada era, including the challenges of the MILF 

and the ASG in the south. Closely associated with former President Fidel Ramos, 

one of her principal supporters and advisors, her policies refl ected continuity with his 

administration rather than the Estrada administration-toward the south as well as the 

rest of the country.598

594 International Crisis Group, “Southern Philippines Backgrounder,” 19.

595 Ressa, Seeds of Terror, 136 – 137.

596 Symonds, “Political Origins and Outlook of Jemaah Islamiyah,” Part 3, 3.

597 The New Filipino Movement, “President Joseph Ejército Estrada,” Neofi noy.info. URL: http://www.

neofi noy.info/The%20RP%20Presidents/estrada.htm. Accessed: September 5, 2005.

598 The New Filipino Movement, “President Gloria Macapagal-Arroyo,” Neofi noy.info. URL: http://

www.neofi noy.info/The%20RP%20Presidents/arroyo.htm. Accessed September 5, 2005.
216

Briefl y stated, her policies were (1) renewal of the peace process with the MILF, 

(2) a search for new leadership of the MNLF as a prelude to facilitating MILF/MNLF 

cooperation, and (3) “total war” against the ASG and ending the type of terrorism 

it represented.599 Soon after her installation as President she declared a unilateral 

cease-fi re and initiated exploratory talks with the MILF aimed at renewing the former 

mutual cease-fi re agreement originally made by President Ramos in 1997.600 Such 

an agreement was reached and signed in Kuala Lumpur, Malaysia, on March 24, 

2001.601 Further talks and agreements on various issues such as security, humanitarian 

assistance, and economic development continued throughout 2001 and into 2002. An 

MILF condition for these talks was that they be mediated by the OIC and that they be 

conducted in an OIC country. The Malaysian government of Mahathir Mohamed took 

an active role in facilitating this process, as did the Libyan government of Mu`ammar 

Qadhafi .602 A fi nal aspect of these talks was an agreement, signed in Kuala Lumpur in 

August 2001, between the MILF and MNLF stating their intention to reunify after a 

separation of nearly 20 years.

Another Arroyo initiative was to schedule the long-delayed plebiscite, required by 

the Philippine Constitution, to formalize the expanded ARMM agreed on in the 1996 

Jakarta Agreement. This she put on the calendar for August 2001, three months prior to 

the scheduled gubernatorial elections for the ARMM in November 2001.603 One who 

opposed this process as well as the central role being played by the OIC in the talks 

between the government and the MILF was MNLF leader and ARMM governor Nur 

Misuari. Misuari’s opposition to the Arroyo peace process provoked a split within the 

15-man MNLF Executive Council that Arroyo effectively managed to secure the ouster 

of Misuari as MNLF chairman in April 2001 and his replacement by Parouk Hussein. 

Hussein later won election in November as the new governor of the ARMM.604

The Demise of Nur Misuari

The eclipse of Misuari was complete. His ultimate success in emerging as the 

governor of the ARMM in 1996 had been in fact the beginning of his downfall. Although 

simultaneously serving as Chairman of the SPCPD that gave him oversight of the 

expenditure of large amounts of development funds for the southern Philippines, there 

was a widespread perception that many of these funds had been squandered on large 

“showcase” projects or support of Misuari’s own profl igate lifestyle, and too little had 

been spent on health services, literacy, problems of malnutrition and infant mortality, 

599 Manalo, “The Philippine Response to Terrorism,” 5.

600 United States Institute of Peace, “The Mindanao Peace Talks: Another Opportunity to Resolve the 

Moro Confl ict in the Philippines,” Special Report 131 (Washington, DC: United States Institute of Peace, 

January 2005), 6. Also Mel C. Labrador, “The Philippines in 2001: High Drama, a New President, and 

Setting the Stage for Recovery,” Asian Survey, XLII, 1 (January/February 2002), 146.

601 International Crisis Group, “Southern Philippines Backgrounder,” 32.

602 USIP, “The Mindanao Peace Talks,” 6.

603 Manalo, “The Philippine Response to Terrorism,” 5.

604 Abuza, Militant Islam in Southeast Asia, 43.
217

or in employment creation.605 Salamat Hashim’s MILF, moreover, had long opposed 

Misuari’s leadership, and the MILF had only grown stronger since 1996, especially in 

Mindanao, where the MILF assertion of independence against Misuari’s acceptance of 

autonomy led many to accuse the latter of having sold out to the Philippine regime for 

his own personal benefi t. The rallying of many Misuari followers, including some who 

had been integrated into the Philippine security services under the terms of the Jakarta 

Agreement, to the MILF during the 2000 fi ghting while Misuari remained loyal to the 

government also had weakened his degree of support. Finally, his failure or inability 

to deal effectively with the Abu Sayyaf threat, particularly in Sulu, his own territory, 

where the Sipidan Island hostages had been held, caused Arroyo and perhaps even the 

Malaysian government, whose seven hostages he had been unable to liberate, to lose 

confi dence in him.

Ousted from the leadership of the MNLF, Misuari soon went into opposition, 

formally denouncing the Arroyo administration in late October 2001, a month prior 

to the ARMM elections, and threatening to take up arms again.606 Coming as it did 

shortly after the September 11, 2001, al-Qa'ida attack on the World Trade Center 

and the Pentagon in the United States, and at a time when the Arroyo administration 

was seeking to cooperate with the United States in its rapidly emerging “global war 

on terrorism,” Misuari’s stance could not have been more ill-timed. A bombing in 

Zamboanga City that killed fi ve on October 28, 2001, attributed to the ASG, just at 

the moment Misuari was expressing his opposition to the Arroyo government, also 

seriously undermined his credibility. 

Undeterred, Misuari succeeded in raising 400 – 600 loyalists who on November 19 

attacked several military posts in Jolo in an effort to halt the gubernatorial election 

scheduled for November 26. President Arroyo ordered “full force” to be employed 

in suppressing the Misuari rebellion, and in a week of fi ghting nearly 1,300 were 

estimated to have been killed prior to the election. A court order for his arrest having 

been issued, Misuari fi nally fl ed the country, but was detained by Malaysian authorities 

as he tried to land in Sabah and later extradited to Manila to stand trial.607 His long 

run as the favored leader of the Moro resistance movement by the OIC had come to an 

end. Despite the violence, elections were held as scheduled on November 26, and new 

MNLF leader Parouk Hussein, with the full support of the Arroyo administration, was 

duly chosen as the new governor of the ARMM.

Abu Sayyaf Again

Misuari’s cause probably was not helped by yet another major ASG kidnapping and 

hostage crisis that had emerged earlier in the year. As reported by CNN correspondent 

Maria Ressa,

605 Abuza, Militant Islam in Southeast Asia, 42.

606 Turbiville, “Bearers of the Sword,” 7.

607 Abuza, Militant Islam in Southeast Asia, 43.
218

On May 27, 2001...Khadaffy Janjalani’s group [on Basilan Island] used 

one of the high-speed boats bought by the Sipidan ransom money to get 

to the southern Philippine Island of Palawan...In the middle of the night, 

armed men stormed the rooms by the ocean of the Dos Palmas resort, 

pulling out twenty people, including three Americans...By June 1, the 

groups had landed on the island of Basilan and kidnapped still more 

hostages from the Golden Harvest plantation. Pursued by the Philippine 

military, the Abu Sayyaf and their hostages fl ed to a hospital and church 

compound in the town of Lamitan, where a day-long siege ended in a 

fi asco that spotlighted either the incompetence of the Philippine military 

or collusion and corruption on a massive scale.608

Totally surrounded by more than 1,000 soldiers, Ressa goes on to say, a back 

entrance of the church was left unguarded after dusk, enabling the apparently informed 

kidnappers and their hostages to simply walk out of the compound and disappear into 

the jungle.

The hostage crisis that ensued ended more than a year later, on June 7, 2002, when 

a Philippine Army operation, supported by U.S. soldiers who now were providing 

intelligence and training to the Philippine units, managed to rescue the one remaining 

living hostage, an American, Gracia Burnham, whose husband, Martin Burnham, along 

with a Filipina nurse, Edilborah Yap, were killed in the course of the operation.609 In 

the meantime, the crisis provoked severe recriminations within the Philippine Army 

and government as well as among the public, especially when an investigation into 

the church escape fi asco held no one accountable.610 Unable to negotiate a ransom 

agreement with either the Philippine or American government, as their colleagues 

had done with the Sipidan hostages a year before, the ASG kidnappers embarked 

on a killing spree, attacking a number of Christian villages on Basilan Island and 

gradually killing several of their hostages, often by cruel torture, and releasing others 

until only the three were left that the Philippine Army tried to rescue in June 2002. 

The Zamboanga City bombing of October 28, 2001, that so compromised Misuari’s 

campaign of opposition against the government was also probably a part of this regime 

of terror.

The Plebiscite of August 2001

Despite the crisis provoked by the ASG kidnapping, Arroyo proceeded with the 

August 14, 2001, plebiscite on expansion of the ARMM. In Senate Bill 2129, passed in 

January, just after her assumption of the Presidency, the government had expanded the 

potential ARMM to 15 provinces and 14 cities in a gerrymandering effort to increase the 

608 Ressa, Seeds of Terror, 116 – 117.

609 The complete story is told in Ressa, Seeds of Terror, 104 – 123.

610 Ressa, Seeds of Terror, 118.
219

likelihood that most of the Muslim region would fall under the ARMM-a step deemed 

necessary to comply most effectively with the spirit of the 1976 Tripoli Agreement 

and the 1996 Jakarta Agreement. Although Arroyo campaigned in 11 provinces and 

14 cities for their inclusion in the ARMM, the results proved disappointing to both 

the President as well as to Muslim leaders in that only Basilan Island (excluding the 

municipality of Isabela) and Marawi City voted to be included together with the four 

provinces previously included in the ARMM in 1989.611 Christian majorities and/

or Muslims disgruntled with the MNFL or MILF in the remaining ten provinces 

simply opposed becoming part of an autonomous Moro Muslim state as envisioned 

by the Tripoli Agreement of 1976, which the government of Gloria Macapagal-Arroyo 

had now accepted.

9/11

Such was the situation in the Philippine Muslim south when, after the September 

11, 2001, al-Qa'ida attacks in the United States, President Arroyo was asked for 

Philippine help in supporting the U.S.-led global war on terrorism. Arroyo was eager 

to cooperate with the United States, and in fact was the fi rst Asian leader to have 

called U.S. President Bush in the wake of the attacks, but a return of U.S. forces to 

the Philippines after their departure from Clark Air Force Base and Subic Bay Naval 

Station in 1992 was a diffi cult political issue for the new President. Too, although 

she was pleased to receive help in combating the ASG organization, she at the same 

time did not want a renewed relationship with the United States to complicate her 

concerted effort to negotiate a fi nal settlement of the long-standing Moro problem in 

the south that she felt was now in sight. For his part, MILF leader Salamat Hashim 

articulated the right words, when on October 8, 2001, the day after the fi rst U.S. strikes 

in Afghanistan aimed at dislodging the Taliban government and destroying the alQa'ida organization, he rejected Usama bin Ladin’s call for a general Muslim jihad

against the United States and its allies and stated that the MILF continued to respect 

the cease-fi re agreement with the government of the Philippines and looked forward to 

peace talks with the government in Kuala Lumpur scheduled for October 15.612

Renewed Relations with the United States

In November 2001, during her fi rst state visit to the United States to commemorate 

the 50th anniversary of the U.S.-Republic of the Philippines Mutual Defense Treaty, 

Bush and Arroyo issued a joint statement in which the two leaders “agreed that the 

September 11 terrorist attacks on the United States and the terrorist activities of the 

Abu Sayyaf Group or ASG (which now hold both Filipino and American hostages in 

the southern Philippines) underscore the urgency of ensuring that the two countries 

611 Labrador, “The Philippines in 2001,” 147.

612 Abuza, Militant Islam in Southeast Asia, 99.
220

maintain a robust defense partnership into the 21st century.”613 Bush had promised 

both military and economic assistance and help “in any way she suggests in getting rid 

of the Abu Sayyaf.”614 Arroyo herself was elated at her reception in the U.S. capital, 

telling reporters after one of her meetings in Washington that she was “at $4 billion 

and counting.”615

The details remained to be worked out but became apparent in December, when 

Manila began allowing U.S. forces to overfl y Philippine airspace and use airfi elds 

as transit points in support of Operation ENDURING FREEDOM in Afghanistan. 

In return, the United States agreed to provide antiterrorism training and advice to 

Philippine military forces engaged in combat operations against the ASG.616 The 

agreement gave rise to a joint exercise called Balikatan (Shoulder-to-Shoulder) 

02 – 01, which brought U.S. troops to Zamboanga and Basilan Island during the period 

February-July 2002. Initially composed of 660 troops, including 200 members of the 

U.S. Special Forces, the group later grew to nearly 1,000 soldiers by the end of the 

exercise. Despite speculation that “shoulder-to-shoulder” meant that U.S. soldiers 

would accompany Philippine Army units on their patrols in search of ASG fi ghters, the 

U.S. role remained confi ned to training, advising, and intelligence support based on 

aerial reconnaissance of Basilan Island and surrounding regions. Indeed, the mission 

of the U.S. forces was very narrowly circumscribed in order not to violate provisions 

of the Philippine Constitution that prohibited the stationing of foreign forces on 

Philippine soil.617 In January 2002, moreover, prior to the deployment of the U.S. 

forces, the United States, Arroyo’s government, and the MILF had signed a trilateral 

agreement that U.S. forces would not enter MILF-controlled territories on Basilan or 

elsewhere in the Philippines in pursuit of ASG fi ghters, much to the chagrin of some 

in both the U.S. and Philippine armed forces.618

Confi ned to Basilan Island, Operation Balikatan 02 – 01 had some success in 

capturing or killing a number of ASG fi ghters and in bringing an end to the Dos 

Palmos kidnapping crisis, when on June 7, 2002, the Philippine Army was able to 

deliver to U.S. forces the one remaining American hostage, Gracia Burnham. Most 

ASG members, including Khaddafy Janjalani, managed to elude the search and 

destroy mission organized against them and escape, mainly to Sulu, but also into safe 

havens in Mindanao, where U.S. forces, by the terms of reference of their presence in 

613 The White House, “U.S.-Philippine Joint Statement on Defense Alliance.” November 20, 2001. URL: 

http://www.whitehouse.gov/news/releases/2001/11/20011120.html. Accessed: September 5, 2005.

614 Sonya Ross, “Bush Promises Help Against Philippine Terrorists,” Honolulu Advertiser, November 

21, 2001.

615 James Hookway, “Manila Proves Key U.S. Ally in Terrorism War-Bush Responds with Aid, but 

There are Limits to Philippine Support,.” Wall Street Journal, November 20, 2001.

616 Angel Rabasa, “Political Islam in Southeast Asia: Moderates, Radicals and Terrorists,” Adelphi 

Papers (London: International Institute for Strategic Studies, July 1, 2003), URL: http://www3.oup.co.uk/ 

adelph/hdb/volume_358/Issue_011. 617 Michael J. Montesano, “The Philippines in 2002: Playing Politics, Facing Defi cits, and Embracing 

Uncle Sam,” Asian Survey, XLIII, 1 (January/February 2003), 161 – 162.

618 Abuza, Militant Islam in Southeast Asia, 48.
221

the Philippines, were unable to go. The ASG retaliation was fi erce, however, as strings 

of urban bombings occurred with regularity throughout the southern Philippines and 

also in Manila throughout 2002 and into 2003, including one on October 2, 2002, in 

Zamboanga City, in which a U.S. serviceman was killed. Later evidence collected 

from captured terrorists determined that various Indonesian members of Jemaah 

Islamiyah had actively collaborated with the ASG in perpetrating these bombings,619

although the campaign appeared to have been directed by Khaddafy Janjalani.620

Despite MILF denials of any connection with these terrorist attacks and indeed formal 

condemnation of them, mounting evidence of established relations between the MILF 

and various Jemaah Islamiyah fi ghters operating in the Philippines kept the MILF on 

the defensive.

The overall lack of success of Operation Balikatan 02-01 led the United States and 

the government of the Philippines to undertake Operation Balikatan 03-01 the following 

year, this time with the focus on Jolo and the Sulu Archipelago, where about 350 U.S. 

Special Forces personnel were deployed in February 2003 along with approximately 

1,000 U.S. Marines positioned on ships offshore. During this campaign, U.S. forces 

reportedly had been quietly authorized by the Arroyo government to engage in combat 

operations against ASG forces, despite the fact that such an authorization would 

technically be in violation of the Philippine Constitution.621

Who Is In Charge?

Growing disarray in the Arroyo administration was evident in early 2003. The 

last week of 2002 had seen a series of murderous attacks in civilian targets in several 

provinces of Mindanao that the Army high command blamed on the MILF, despite 

adamant denials from Salamat Hashim and other MILF leaders. Meanwhile, since 

mid-October 2002, Arroyo, who on December 31, 2002, formally announced that 

she would not be a candidate in the next Presidential elections scheduled for May 

2004, was engaged in peace talks with the MILF in Malaysia that she deemed to be 

proceeding well. She also continued successfully to urge the United States not to add 

619 The continuing violence in the southern Philippines was overshadowed by the August 12, 2002, 

bombing of the Sari nightclub in Denpasar, Bali, in neighboring Indonesia that killed 202, including 88 

Australian tourists. The Bali bombing was the world’s deadliest terrorist incident since the September 11, 

2001, attacks on New York and Washington. Largely overlooked at the time were the almost simultaneous 

bombings that same evening of the U.S. consulate in Bali and the Philippine consulate in Manado, the 

Indonesian city closest to the Philippines. The Bali bombing was immediately understood to be the work 

of Jemaah Islamiyah, and the simultaneity of the other two bombings suggests they were part of the same 

operation. Later arrests of nearly 30 individuals believed to be associated with the bombings brought to light 

the fact that many had trained in MILF camps in Mindanao. Although the MILF may have only “hosted” 

their training, the only reasonable analytical conclusion was that linkages existed between the MILF and 

the Jemaah Islamiyah that conjoined their respective struggles as parts of a common cause or were simply 

separate manifestations of the same cause. Montesano, “The Philippines in 2002,” 135. 

620 International Crisis Group, “Southern Philippines Backgrounder,” 22 – 24.

621 Michael J. Montesano, “The Philippines in 2003: Troubles, None of Them New,” Asian Survey, 

XLIV, 1 (January/February 2004), 100.
222

the MILF to the list of Foreign Terrorist Organizations,622 while in February 2003, 

concurrent with the redeployment of U.S. forces to Sulu for Operation Balikatan 

03-01, she presented the Army command with a three-month deadline to “break the 

back of the ASG.”623

Apparently without specifi c Presidential authorization, but acting on these general 

orders, on February 11, 2003, the Army launched a multi-battalion assault on the 

“Buliok Complex,” a series of towns in the Liguasan Marsh near Pikit, the hometown 

of Salamat Hashim, southeast of Cotabato City, where the MILF had reestablished its 

headquarters after the loss of Camp Abu Bakar in 2002.624 Hardly had the operation 

begun, however, when President Arroyo issued orders for the military to halt the 

attack, because the government had approved the fi nal draft of a comprehensive peace 

agreement with the MILF. On the following day, the President suddenly reversed her 

decision and ordered the Army to capture and occupy the Buliok Complex-but only to 

capture the Pentagon Gang, an independent and particularly brutal ASG-like terrorist 

group that the Army insisted was being given refuge there.625

The Pentagon Gang continued to operate in 2005, meaning that the Army did not 

succeed in its stated mission, but it did succeed in occupying the Buliok Complexprobably the real intent of the operation-over which the Philippine fl ag was raised on 

February 14 after the dispersal of an estimated 1,500 MILF fi ghters and about 40,000 

civilian refugees.626 Following the fall of the Buliok Complex, Mindanao was struck 

with a series of violent terrorist attacks, the most notable of which were the bombings 

of Davao International Airport on March 4, 2003, and the Davao wharf at Sasa on 

April 2, 2003, in which 38 were killed and over 200 wounded.627 The Army adamantly 

argued that the MILF was behind these attacks, whereas the “MILF consistently and 

vociferously denied complicity” in any of these attacks.628 The situation was admittedly 

confused by the reported arrival in Mindanao at this time of ASG leader Khaddafy 

Janjalani and many of his fi ghters who were escaping growing pressure on them from 

Operation Balikatan 03-01 in Sulu.629

Clearly frustrated by the contradiction between her policy of trying to negotiate with 

the MILF and that of the Army to pursue the organization as aggressively as possible, 

622 Michael J. Montesano, “The Philippines in 2002,” 165 – 166.

623 Anthony Davis, “Resiliant Abu Sayyaf Resist Military Pressure,” Jane’s Intelligence Review, 15, 9 

(September 2003), 14.

624 International Crisis Group, “Southern Philippines Backgrounder,” 7.

625 Ressa, Seeds of Terror, 141.

626 Anthony Davis, “Philippine Army Prevents MILF Reorganization,” Jane’s Intelligence Review, 15, 

3 (March 2003), 16.

627 International Crisis Group, “Southern Philippines Backgrounder,” 23.

628 Anthony Davis, “Fragile Ceasefi re Holds Out in the Philippines,” Jane’s Intelligence Review, 16, 1 

(January 2004), 16.

629 Anthony Davis. “Philippines Fears New Wave of Attacks by Abu Sayyaf Group” Jane’s Intelligence 

Review, 17, 5 (May 2005), 11.
223

on May 7, 2003, on the eve of her departure for her second state visit to Washington, 

Arroyo called on the MILF to “renounce all terrorist ties” or risk designation as a 

Foreign Terrorist Organization by the United States.630 Salamat and other MILF 

spokesmen quickly did so, noting that “the MILF, as a liberation organization, has 

repeatedly renounced terrorism publicly as a means of obtaining political ends.” 

Arroyo’s visit to the United States at this time was closely linked to U.S. efforts to 

gain Philippine support for Bush administration policy in Iraq, which U.S. forces had 

occupied in March, and she was able to obtain a number of favorable concessions, 

including keeping the MILF off the Foreign Terrorist Organization list.631 Soon after 

her return from Washington, Arroyo again met Malaysian Prime Minister Mahathir 

Mohamed in Tokyo, and on July 19, 2003, through the good offi ces of the government 

of Malaysia, a new Mutual Cessation of Hostilities agreement was signed between the 

MILF and the government.632

At this point, two key developments intervened. A military mutiny in Manila on 

July 27 called for Arroyo’s own resignation as well as that of her Defense Secretary, 

General Angelo Reyes, and the Armed Forces intelligence director, Victor Corpus. 

Accusing them of staging bombings in Mindanao for the purpose of securing increased 

American military and economic assistance and of selling arms to Muslim rebels for 

personal profi t, the rebels asserted that they could no longer serve such a corrupt 

government at such low pay.633 Perceiving a plot within the Army to overthrow 

her, Arroyo moved adroitly to secure the resignations of both Reyes and Corpus in 

August.634 Widely perceived as a “hawk” over issues of war and peace in Mindanao, 

Reyes was replaced by another retired general, Edwardo Ermita, who previously 

had been serving as Arroyo’s point man in the peace process with the MILF and the 

communist New People’s Army (NPA). As chief negotiator with the MILF, Arroyo 

appointed Silvestre Afable, previously the head of her Presidential management staff, 

whom she believed the MILF respected and trusted.635

630 International Crisis Group, “Southern Philippines Backgrounder,” 7.

631 Montesano, “The Philippines in 2003,” 100. Among the concessions received were designation of 

the Philippines as a “major non-NATO ally” of the US, creation of a new combat engineering unit and other 

counterterrorism support for the Philippines Armed Forces, twenty refurbished helicopters, development 

assistance for Mindanao and fi nancial support for the Philippines-MILF peace process, improved processes 

for overseas workers’ remittances, aid for Filipino veterans of the U.S. military, and Generalized System of 

Preferences benefi ts for selected Philippine exports to the United States.

632 International Crisis Group, “Southern Philippines Backgrounder,” 7.

633 The issues raised by the mutineers were clearly related to a new book that had appeared in the summer 

of 2003 by Gracia Burnham, In the Presence of My Enemies (Carol Stream, IL: Tyndale House Publishers, 

2003). Ms. Burnham, who had been an Abu Sayyaf kidnapping victim for more than a year prior to her 

being freed by the Philippine Army on June 7, 2002, had written that certain Philippine Army members had 

connived with her ASG captors to divide millions of dollars the group had raised through their kidnapping 

operations. See Leslie Davis, “Philippines on Trial over Hostage Issue,” Asian Times, August 7, 2004. URL: 

http://www.atimes.com/atimes/Southeast_Asia/FH07Ae05.html. Accessed September 22, 2005.

634 Montesano, “The Philippines in 2003,” 96 – 97. 

635 Davis, “Fragile Ceasefi re Holds Out in the Philippines,” 16.
224

Death of Salamat Hashim

The second development was the death (by heart attack) of MILF Chairman 

Salamat Hashim on July 13, 2003, nearly a week before the signing of the new Mutual 

Cessation of Hostilities Agreement. Although announcement of his death was delayed 

until August 5, when it could be said that Haj Ali Murad had succeeded Hashim as 

Chairman of the MILF, the choice of Murad was positively received by the Arroyo 

administration. Long the MILF chief of military operations who had remained most 

of his life in Mindanao, he lacked the strong international connections possessed 

by Hashim, and was considered less a religious ideologue than his predecessor had 

been.636 Because Murad was considered an easier leader to deal with, despite his 

formidable talents as a military commander, Arroyo was optimistic, given the new 

team of Philippine negotiators she was putting in place, that a fi nal settlement of the 

Moro problem could be readied.

Although the cease-fi re with the MILF continued to hold up through 2005, further 

negotiations aimed at reaching a fi nal settlement failed to occur quickly. First, there 

was the need for Haj Ali Murad to take charge of the organization he now headed. The 

refusal of the Army to withdraw from the Buliok Complex it had taken in February, 

a condition set by the MILF, also delayed the resumption of negotiations. So too did 

the MILF demand for charges to be dropped against 150 MILF leaders accused of 

organizing the terrorist attacks that had followed the Army’s storming of the Buliok 

Complex. Yet another issue was an MILF demand that third-party cease-fi re monitors 

from OIC countries, primarily Malaysia, be permitted to enter Mindanao prior to 

the start of negotiations. Although the Arroyo administration agreed to permit such 

a team to visit the MILF area on a temporary basis to assess the situation and make 

recommendations to the government, its position was that a permanent observation 

team could only be permitted after the conclusion of a fi nal agreement, when its 

function would be to monitor implementation of the agreement.637

Government-MILF Talks Begin

These issues were fi nally resolved, and the fi rst of six rounds of exploratory 

talks in Kuala Lumpur during 2004 took place in February 2004. Further rounds of 

talks continued in February, April, and September 2005. Until this point, the talks 

remained “exploratory’’ only, and although both parties expressed the desire to enter 

formal negotiations to reach a fi nal peace settlement, a variety of issues continued 

to intervene to retard the process. The question of OIC-sponsored multinational 

observers was addressed in the fi rst meeting in February 2004, and the fi rst team 

636 International Crisis Group, “Southern Philippines Backgrounder,” 9.

637 Davis, “Fragile Ceasefi re Holds Out in the Philippines,” 16 – 17.
225

consisting of Malaysian, Brunei, and Libyan observers/monitors arrived in Mindanao 

in October.638

A complicating issue was a United States initiative to become part of the peace 

process. During her May 2003 visit to Washington, President Arroyo had asked for 

and had received from U.S. President George W. Bush a promise of fi nancial support 

for the Philippines-MILF peace process. Thirty million dollars were made available 

and provided to the Washington-based United States Institute of Peace (USIP) to help 

facilitate the peace process. Efforts to enter the peace talks in Kuala Lumpur, however, 

were rebuffed by the Malaysian government and the OIC. The high-level team put 

together by the USIP, consisting of former U.S. ambassadors to Manila and others, 

therefore, had to content itself with bilateral meetings with Philippine government and 

MILF representatives engaged in the peace talks as well as with individual Filipino 

scholars and civil society activists engaged in promoting peace.639 The Institute also 

sought to promote dialogue through research and the holding of seminars on key issues 

pertinent to the confl ict. A major example was a two-day workshop on the thorny 

issue of ancestral domain held on May 24-27, 2005, in Davao City and attended by 

nearly 40 participants, including Philippine government and MILF representatives, 

Philippine scholars, and civil society activists.640

The Issues at Stake

Ancestral domain claims, along with security and the economic redevelopment 

of the southern Philippines after the conclusion of peace, emerged as the three major 

issues to be resolved in the exploratory talks in Kuala Lumpur prior to moving 

into fi nal peace talks.641 Superfi cially, security seemed to be the easiest issue to 

resolve. Early in the talks, the two parties established a series of joint Coordinating 

Committees on the Cessation of Hostilities (CCCH) to coordinate issues arising 

from the July 2003 cease-fi re agreement and to react jointly to cease-fi re violations, 

when they occurred. 71 cease-fi re violations in 2004, as opposed to 559 in 2003, 

were dealt with in this manner.642

638 Temario C. Rivera, “The Philippines in 2004: New Mandate, Daunting Problems,” Asian Survey, 

XLV, 1 (January/February 2005), 127.

639 Eugene Martin, “U.S. Interests in the Philippine Peace Process,” United States Institute of Peace web 

page, February 8, 2005. URL: http://www.usip.org/Philippines/reports/mindanao_martin.html. Accessed 

September 22, 2005.

640 For the proceedings of the conference, see Astrid S. Tuminez, “Ancestral Domain in Comparative 

Perspective,” Special Report 151, United States Institute of Peace web site. URL: http://www.usip.org/pubs/

specialreports/sr151.html. Accessed September 22, 2005.

641 Rivera, “The Philippines in 2004,” 127.

642 Embassy of the Philippines (Washington), “Status of the GRP-MILF Peace Process,” United States 

Institute of Peace web site, February 5, 2005. URL: http://www.usip.org/philippines/reports/ rosario.pdf. 

Accessed September 22, 2005. 
226

Security. Although instances of terrorist violence were signifi cantly reduced 

during this period, at least three major terrorist attacks, each eventually attributed to 

the ASG with JI support, marred the security environment. The fi rst, on February 27, 

2004, as the fi rst government-MILF talks were getting underway in Kuala Lumpur, 

was the bombing of a superferry off Corregidor Island as it departed Manila for 

Davao City in Mindanao, killing over 100.643 The second, on February 14, 2005, 

again as talks were resuming in Kuala Lumpur, which an ASG spokesman called a 

“Valentine’s Day gift to Mrs. Arroyo,’’ consisted of virtually simultaneous bombings 

in the Makati fi nancial district of Manila, General Santos City, and Davao City that 

claimed 12 killed and at least 140 wounded.644 The third, on August 28, 2005, was 

another bomb blast on a ferry, the Doña Ramoña, departing Lamitan on Basilan 

Island for Manila, wounding 30.645 These and lesser instances of violence continued 

to provoke Philippine government intervention and claims that the MILF continued 

to harbor terrorists, despite adamant MILF denials and continued cooperation with 

the government to uncover wanted individuals.

Increased government success in capturing or killing various ASG and JI fi ghters 

during the new cease-fi re era was indicative of increased cooperation.646 Philippine 

government security operations remained intrusive, however, and MILF spokesmen 

often accused government forces of being in violation of the Cessation of Hostilities 

Agreement more often than its own “renegade’’ commanders. Examples occurred 

on November 19, 2004, and January 27, 2005, when on both occasions Philippine 

military helicopter gunships and aircraft on the basis of “solid intelligence’’ attacked 

villages in MILF territories in which ASG leaders, including Janjalani, were alleged 

to be meeting with JI operatives from Indonesia to plan future operations. On both 

occasions, civilian villagers were killed, but the intended targets were not included 

643 Sol Jose Varizi, “Abu Sayyaf: From Kidnap to Genuine Terror,” Philippine Headline News Online, 

August 26, 2004. URL: http://www.newsfl ash.org/2004/02/22/hl/hl100913.htm. Accessed September 22, 

2005. 

644 Anthony Davis, “Filipinos Fear New Wave,” Jane’s Intelligence Review, 17, 5 (May 2005), 10. Also 

“New Abu Sayyaf,” The Economist, February 17, 2005. URL: http://www.economist.com/ Printerfriendly.

cfm?Story_ID=3675637. Accessed September 22, 2005. Also AFP, Manila, “Abu Sayyaf, Army Clash on 

Strife-torn Philippine Island,” Taipei Times, February 20, 2005. URL: http://www.taipeitimes.com/News/

world/archives/2005/02/20/200223815/print. Accessed September 3, 2005.

645 Associated Press, “30 Wounded in Blast on Philippines Ferry,” International Herald Tribune, AsiaPacifi c edition, August 29, 2005. URL: http://www.iht.com/articles/2005/08/28/news/phils.php. Accessed 

September 20, 2005.

646 Among those captured/killed were: Toufi k Rifqi, Indonesian, captured October 2003; Fathur Rohman 

al-Ghozi, Indonesian, killed October 2003; Galib Andang (Commander Robot), ASG commander on Jolo 

Island, captured December 2003; Hamsiraji Sali, ASG leader in Basilan, killed with fi ve of his men in 

April 2004; three Indonesians with ASG Filipino guide, captured December 2004; ASG operatives Gamal 

Baharan and Abu Khalil Trinidad, captured February 2005; ASG fi ghter Gappal Banna, arrested in March 

2005; Indonesian JI operative Zaki, captured in March 2005; ASG bomber Alex Kahal, captured in August 

2005; among others. In April 2005, more than 800 alleged militant Muslims, members of the ASG and 

others, were reported to be imprisoned in Bicutan military camp near Manila. Maulana Alonto, “Sulu 

Fighting Exposes Filipino Government Claims to Want Peace in Mindanao,” Al-Jazeersh.info, April 5, 

2005. URL: http://www.maranao.com/articles/Sulu%20fi ghting%20exposes%20Filipino%20government 

%20claims.htm. Accessed September 26, 2005.
227

among the casualties.647 Despite the agreements on security cooperation, the security 

situation in the south remained tense and the parties distrustful of one another.

Agreement on the OIC-sponsored International Monitoring Teams (IMT) that fi nally 

arrived in October 2004 was meant to interpose a third party, trusted by both sides, as 

a mechanism for ameliorating the distrust between the MILF and the Army. The teams 

were trusted by the MILF that had demanded their presence as a condition for entering 

exploratory talks with the government. At the same time, they were trusted by the 

Arroyo administration on the basis of the President’s relations with Malaysian Prime 

Minister Mahathir Mohamed and, after October 2003, Abdullah Ahmad Badawi. The 

positive effect of the IMT was not immediately apparent in the months immediately 

after their deployment, however. Whether a third party could play such a role over the 

longer term remained to be seen.

One remaining diffi culty with the OIC role was that, despite its efforts to facilitate 

talks between the government and the MILF, it still recognized the MNLF (if not Nur 

Misuari) as the offi cial voice of the Bangsamoro people.648 Still technically the elected 

leadership of the ARMM, now under Parouk Hussein, Philippine government, OIC, 

and MNLF leadership policy was for the MILF ultimately to rejoin and become part 

of an enlarged MNLF. Meanwhile, the MNLF leadership was being challenged by a 

breakaway group (MNLF-BG), still loyal to Nur Misuari (who remained under house 

arrest in Santa Rosa) but headed by religious leader Habier Malik. This group engaged 

the Philippine Army in pitched battles on Jolo Island in February 2005.649 Despite the 

MILF-government agreement on security cooperation, security in the south remained 

tenuous in ways over which the MILF had no control.

Economic Redevelopment. On the second issue of economic redevelopment of 

the southern Philippines, the MILF and the government reached ready agreement in 

principle, although concerted efforts to spur reconstruction in the south necessarily 

awaited a fi nal peace settlement. Early in the negotiations, agreement was struck on 

647 Anthony Vargas, “AFP Checking Report Janjalani Killed in Air Raid,” The Manila Times, December 

21, 2004. URL: http://www.manilatimes.net/national/2004/dec/21/yehey/top_stories/ 20041221tops.html. 

Accessed September 20, 2005. Also Roel Pareña, “AFP Launches Airstrikes on Janjalani Meeting,” Star

(Manila), January 28, 2005. URL: http://www.newsfl ash.org/2005/02/hl/ hl101697.htm. Accessed September 

20, 2005. Also USIP, “The Mindanao Peace Talks,” 11.

648 USIP, “The Mindanao Peace Talks,” 10.

649 Davis, “Filipinos Fear New Wave,” 10. AFP Manila, “Abu Sayyaf, Army Clash on Strife-torn 

Philippine Island,” Taipei Times, February 20, 2005. URL: http://www.taipeitimes.com/News/world/ 

archives/2005/02/20/2003223815/print. Accessed September 3, 2005. 
228

the creation of a Mindanao Trust Fund (MTF).650 Under the terms of this agreement, 

a Joint Needs Assessment was conducted by the World Bank during August and 

September 2004 in which needs were assessed in four areas: human development, 

rural development, fi nance and private sector, and governance and institutions.651 Also 

created was a Bangsamoro Development Agency (BDA), originally consisting of 135 

personnel identifi ed by the MILF to take the lead in managing development projects in 

the Bangsamoro area. A Malaysian Technical Cooperation Program (MTCP) was also 

established that provided training for the BDA personnel in 2005.652

Easy enough to agree on, perhaps harder to implement, the MTF concept was fraught 

with problems, even before the conclusion of the hypothetical peace settlement. Most 

funds provided by the donor countries were matching funds, meaning that they would 

be made available only to match appropriations by the Philippine government. The 

government, meanwhile, faced a looming fi scal crisis in 2005, brought on by a massive 

budget defi cit and a ballooning public debt, all aggravated by widespread corruption 

throughout the government and society, plus the seemingly unending security problem 

associated with the Moro problem in the south as well as the continuing problem 

with the NPA in the north. The question of authority over the allocation and spending 

of available redevelopment funds, most of which were attached to specifi c projects 

identifi ed by the World Bank, also loomed as a divisive issue. How authority between 

the World Bank, Philippine government ministries, and the newly established local 

BDA in Mindanao-created to provide a stronger sense of Moro self-determination and 

control of their own destiny-would be divided remained unresolved.

Ancestral Domain. The fi nal issue, ancestral domain, on the table for the Kuala 

Lumpur meetings during 2005, promised to be an even thornier problem. Gradually 

driven from their ancestral lands by a hundred years of “colonization’’ by northern 

Christian Filipinos, and by more than 30 years of war since its outbreak in 1972, the 

“ancestral domains’’ of the Moros had all but been lost. Yet, through the MILF, the 

struggle for self-determination and independence continued, not strong enough to claim 

independence by force from the Philippine government, yet strong enough to make it 

impossible for the Philippine government to impose its will on the Moros of Mindanao. 

The MILF no longer claimed the whole of Mindanao, but negotiated in terms of the 

1976 Tripoli Agreement that allocated 13 provinces as the designated homeland of the 

650 Originally called the Multi-Donor Trust Fund, it was put together by the World Bank in cooperation 

with the government of the Philippines during the summer of 2003 for the purpose of consolidating donor 

funds from a variety of countries for the redevelopment of the southern Philippines after a fi nal peace 

settlement had been reached. The Islamic Development Bank, the Organization of Petroleum Exporting 

Countries (OPEC), Bahrain, the United Arab Emirates, Kuwait, and Saudi Arabia were early contributors 

to the fund. Clearly aimed at wooing the MILF into peace talks with the Philippine government, President 

Arroyo advertised it as a “peace dividend” for Mindanao as soon as a peace agreement had been fi nalized. 

Rexcel Sorza, “Life in Mindanao Better Once Peace Talks Start: Manila,” IslamOnline.net, September 26, 

2003. URL: http://islamonline.net/English/ News/2003-09/26/article07.shtml. Accessed September 26, 

2005.

651 USIP, “The Mindanao Peace Talks,” 11.

652 Embassy of the Philippines (Washington), “Status of the GRP-MILF Peace Process,” 3.
229

Moro people. Yet the Philippine constitutional requirement that such an entity could 

be created only by a popular plebiscite in each of the provinces so affected had thus 

far kept this provision of the Tripoli Agreement from being implemented in full. How 

this dilemma would be resolved remained unclear, although talks in September 2005, 

in which the adoption of a federal system for the Philippines was seriously addressed, 

gave hope to delegates from both sides that a fi nal settlement between the government 

and the MILF might be in the offi ng.653

OUTLOOK

Still, the MILF had not abandoned its historic view that independence for the 

Bangsamoro Muslim people was its ultimate objective. Nor had the Philippine 

government backed away from its historic perspective that the south was an integral part 

of the Philippine state and that the rights of the Moro people had to be accommodated 

within the context of the right of all other minorities and indigenous peoples of the 

country. What appears to have become clear, at least to President Arroyo and the MILF 

leadership, was that after more than 30 years of war fi nal victory for either side was 

not possible, and close observers of key actors on both sides affi rmed that the desire 

for peace was authentic.654 Indeed, the desire for peace may be even stronger among 

the Muslim supporters of the MILF, whose cities and rural countryside have been 

ravaged by 30 years of war, with their inhabitants severely displaced, than for the 

government itself. For the government, however, the crisis in the south has involved a 

long and expensive military campaign that has not been effective and that it no longer 

can afford. Both sides appear sincere in their desire for a more or less permanent 

settlement, but on what terms?

The MILF may be content to live indefi nitely with the current cease-fi re, established 

in July 2003, that helps to keep the Philippine Armed Forces at arm’s length. If so, then 

it may avoid reaching a fi nal settlement that likely would defi ne the Muslim south 

as something less than the independent Muslim state for which it has been fi ghting 

for many years. Meanwhile, it will continue to operate its shadow government in the 

south that will be more effective in commanding the allegiance of the Muslims of the 

south than the authorities representing the central government in Manila. Time, for 

the MILF, remains on its side as long as it is not confronted by serious violence. If the 

central government in Manila really wants a less problematic south, it must eventually 

understand that peace will come as a result of permitting a maximum degree of selfdetermination for the Bangsamoro people of the south.

653 Agence France-Presse, “RP-MILF Peace Talks in Malaysia Make Major Breakthrough,” ing7.net, 

September 17, 2005. URL: https://news.inq7.net/breaking/index.php?index=1&story_id250494. Accessed 

September 22, 2005.

654 Zachary Abuza, “Crunchtime for the Mindanao Peace Process,” United States Institute of Peace

web site, February 8, 2005. URL: http://www.usip.org/philippines/reports/mindanao_abuza.html. Accessed 

September 5, 2005.
230

From the point of view of the government in Manila, however, especially under 

Arroyo, a fi nal settlement that retains the south as a part of the Philippines is vital. 

Despite her astute management of the peace process up to this point, the problems 

faced by her administration are manifold and massive, and her hold on political power 

is precarious. Like her mentor, former President Fidel Ramos, she is accused by some, 

particularly in sectors of the military, of “coddling’’ the Muslims unnecessarily. There 

are “spoilers’’ on all sides—the ASG, elements of the MILF disgruntled with Murad’s 

leadership, military factions disgruntled with Arroyo’s leadership, and others—that 

could take some action designed to scuttle the current, very fragile peace process. 

Even if successful, a peace process that did not result in a high degree of perceived 

self-determination on the part of the Moro population will likely leave a restive Muslim 

population under Philippine government rule.

232

Map of Southeast Asia today. Source: CIA.
233

CHAPTER 7

ISLAM AND POLITICS IN SOUTHEAST ASIA

In the West, the domain of religion, represented by the church, and the domain of 

politics, represented by the state, are separate and coexist with their own distinct laws 

and claims of authority...In Islam, however, religion and politics are inseparable.

 —Mir Zahir Husain, 1995

THE FIRST ISLAMIC STATE

The joining of religion and politics has been a feature of Islamic doctrine since 

the establishment of the faith by its Prophet Muhammad beginning in 620 C.E. In 

large measure, this doctrine became implanted because of the example of the Prophet 

himself who, during his lifetime, joined both religious and political authority in his 

own person. As noted by W. Montgomery Watt, Muhammad was both “Prophet and 

Statesman.’’655 The importance of the Prophet’s example (hadith/sunna), moreover, 

in the later elaboration of Islamic law (shari`a) and doctrine virtually guaranteed that 

Muslim scholars would have little choice but to uphold this unity of purpose.

Throughout most of Islamic history, however, this doctrine of the inseparability of 

religious and political authority has been more theoretical than real. Aside from the Shi`a 

faction who hold that the Prophet did indeed designate `Ali bin Abu Talib, his cousin 

and son-in-law, and the latter’s descendants as his heirs in both spiritual and temporal 

authority, most Muslims-the prevailing Sunni majority — have held that the Prophet 

left no clear instructions about how his community should be governed following his 

death, only that it should be guided by the divine revelation that he had received on 

behalf of all mankind. Following a hadith of the Prophet — “My community cannot 

agree on an error.’’ — the close companions of the Prophet after his death chose one 

of their own — “the best among us’’ — as his successor (khalifa/caliph). Although the 

successor Caliph held clear temporal authority, his claim to religious authority became 

increasingly problematic, particularly after the passing of years and the transformation 

of the Caliphate into a dynastic institution in which periodically individuals of an 

impious character held the offi ce.

The Sunni solution was to gradually devolve religious authority on the `ulama, the 

body of professional Islamic scholars who collectively worked to formulate Islamic law 

and doctrine, to propagate it to successor generations, and to implement it throughout 

Islamic society by serving the Caliphs as qadis (judges) in Islamic courts, muftis

(givers of legal opinions) in the Caliph’s courts, and as teachers in madrasas (Islamic 

655 W. Montgomery Watt, Muhammad: Prophet and Statesman (London: Oxford University Press, 

1961).
234

schools). Although religious authority theoretically remained vested in the fi gure of 

the Caliph, in fact it fl owed from the collective consensus (ijma’) of the scholarly 

profession who came to form the lawyer, teacher, and pastoral class in Islamic society 

that was patronized by the Caliphs in return for legitimizing their rule as the “Shadow 

of God on Earth’’ and technically as successor to the inseparable religious and political 

authority of the Prophet Muhammad.

Evolution of the Original Model

The theoretical linkage between religious and political authority became even 

further compromised with the gradual decline of the political authority of the 

Caliphate beginning as early as the second century of the Islamic era, when various 

governors in peripheral parts of the Islamic empire began to succeed in establishing 

dynastic claims of their own. Such dynasties as the Rustamids (777 – 909), Idrisids 

(78 – 926), and the Aghlabids (800 – 909) in North Africa; the Samanids (819 – 1006) 

and Saffarids (867 – 913) in Central Asia and Iran; and the Tulunids (868 – 905) in 

Egypt all continued to recognize the overall religious authority of the Abbasid Caliph 

in Baghdad. In return, the Caliph recognized their local political authority as sultans 

(power holders) as long as they ruled in accordance with Islamic law.

The process of political dissolution of the Caliphate culminated with the establishment 

of the Turkish Seljuk sultanate in Baghdad in 1056. After this time, the former Abbasid 

Empire was in fact a collection of more or less independent sultanates that were only 

theoretically united under the overall authority of the Abbasid Caliph. The ultimate 

demise of the Abbasid Caliphate in 1258 as a result of the sack of Baghdad by the 

Mongol chieftain, Hulagu, grandson of the famous Chengis Khan, was in a sense 

anti-climactic. The offi ce of Caliphate no longer wielded power or even infl uence. 

Islamic (religious) authority was in the hands of the network of `ulama that existed in 

every Islamic sultanate, whereas political and military authority was in the hands of a 

number of dynastic sultanates. The Caliphate was in fact no longer necessary, and no 

serious effort to revive it occurred until the last decades of the 19th century.

Reaction to the End of the Caliphate

It is perhaps the nature of dynastic authority that caused the `ulama, dependent 

as they were on the patronage of the ruler for positions of leadership and authority 

he was able to bestow upon them, to adjust themselves to the changing realities of 

powerholding in the Islamic world. At the same time, so entrenched had the `ulama

become throughout the world that had become Islamic that new sultans coming to 

power generally perceived it in their interest to seek the blessing of the `ulama as a 

basis of their legitimacy as a ruler once the Caliph was not longer present to provide it. 

Such a relationship between the sultan and the `ulama was solemnized by the ceremony 
235

of bai`a (pledge of alliegance)656 that typically inaugurated a new sultan’s rule. In this 

coronation ceremony, as it were, the `ulama formally acknowledged the legitimacy 

of the new sultan, and he in turn committed himself to govern in accordance with 

Islamic law-that is, to rely on the `ulama as the principal administrators of justice, 

education, and religious affairs over which he held legitimate authority accorded him 

by the `ulama.

This revised formula for Islamic governance that had evolved over several centuries 

provided a basis for a renewed expansion of Islam during the 12th-15th centuries C.E. 

In some cases, such as with the Ottoman sultans of Anatonia, the Ghaznavid sultans

of Afghanistan, and the Almoravid and Almohad sultans of Morocco, this expansion 

occurred as a result of renewed military conquest. In many other instances, however, 

as in southeast Asia and Sub-Saharan Africa, it was the result of missionary work by 

traders and traveling `ulama who, as representatives of a dominant, successful, and 

prosperous civilization, succeeded in drawing converts to Islam. The new formula 

whereby an indigenous local ruler could through conversion transform his realm into 

a sultanate, thereby associating himself and his people with the extensive Islamic 

civilization, was a particularly powerful means by which Islam continued to spread 

during the post-Caliphal era.

The Role of Sufi sm

Closely associated with this second expansionist period of Islamic history was 

the fl ourishing of Sufi (mystical) orders associated with Islam during this same era. 

Although the origins of Sufi sm predate this era, most of the great sufi teachers and 

founders of orders — such as al-Ghazali (d. 1111), al-Jilani (d. 1166), al-Rifa’i (d. 

1182), Chisti (d. 1233), al-Suhrawardi (d. 1234), Ibn al-`Arabi (d. 1240), al-Shadhili 

(d. 1258), Rumi (d. 1273), Hajji Bektash (d. 1337), and Naqshbandi (d. 1389) — date 

from the early part of this period.

The growth and widespread acceptance of esoteric Sufi concepts and practices 

added a new dimension to Islam. The diverse approaches represented by the various 

Sufi orders (chanting, singing, dancing, whirling, and silent meditation) to realizing 

direct consciousness of God (Allah), albeit within the confi nes of Islamic doctrine 

and law, added a liberal dimension to the faith that not only respected diversity, but 

honored it. Sufi teaching made it possible to bridge the gap between Islam and other 

religious traditions, facilitating conversion without the necessity of totally abandoning 

pre-Islamic religious practices.

656 The Arabic term bai`a carries the meaning of contract, deal, transaction, or sale, as well as homage or 

pledge of allegiance. In the traditional Islamic states, it represented the “social contract” between the ruler 

and the ruled, as represented by their `ulama.
236

Although later Wahhabi, Salafi , and other religious purists in the 19th and 20th 

centuries would criticize and condemn Sufi sm for enabling non-Islamic concepts and 

traditions to be introduced into Islam, during the post-Caliphal era and prior to the age 

of European colonialism and imperial outreach, the Sufi orders were a source of great 

strength and appeal for Islam, facilitating its spread and widespread acceptance in 

territories far beyond what Marshall Hodgson has called the Islamic Oikoumeni — the 

lands between the Nile and the Oxus.657 The attraction of Sufi stic Islam was not just 

confi ned to the expanding border regions of the Islamic world, however, but became 

a powerful current in the central, historic Islamic lands as well, especially under 

Ottoman rule, until the collapse of the Ottoman empire in the aftermath of World War 

I (1914 – 1918). In many respects, Sufi stic Islam represented the true face of Islam, 

particularly at the popular level, if not at the governmental level, during the postCaliphal era until very recent times. 

SPREAD OF ISLAM TO SOUTHEAST ASIA

As Islam spread in the post-Caliphal era, it nevertheless did so in a fairly common 

political pattern — through the establishment of sultanates, centers of Islamic governance 

by rulers that relied on the `ulama of their realms to uphold their legitimacy and in 

turn empowered the `ulama to administer their realms in accordance with Islamic law 

(shari`a) and custom. This was precisely the pattern that marked the spread of Islam 

in Southeast Asia.

The gradual spread of a network of relatively small, coastal Muslim trading states 

throughout Southeast Asia occurred at the expense of the former Java-based Hindu 

Majapahit kingdom that had dominated most of the southeast Asian archipelago and 

Malay peninsula since the mid-14th century. Majapahit had in turn replaced the even 

stronger and longer-lived Sumatra-based Malay Hindu kingdom of Srivijaya that had 

dominated most of the region since at least the 6th century. Whether one of the new 

Muslim states — perhaps Malacca — would eventually have emerged as a strong new 

state dominating most of the region, displacing Majapahit, cannot be known.

The process of Islamization in Southeast Asia was at this time impacted by the 

arrival of European naval armadas and trading missions. As was noted in the fi rst 

chapter of this study, aside from the Portuguese conquest and capture of Malacca in 

1511, which had the impact of disrupting the unity of the Muslim-dominated trading 

states that had been centered on this strategic port, the European impact in the region 

was not at fi rst great. The Dutch in particular, who eventually came to dominate 

the largest portion of the archipelago, were for more than a century little more than 

just another trading state in the region, albeit a Christian one, headquartered at the 

Company’s fort in Batavia.

657 Marshall G. S. Hodgson, The Venture of Islam: Conscience and History in a World Civilization, Vol 

1, The Classical Age of Islam (Chigago, IL: University of Chicago Press, 1974), 120 – 124.
237

The End of Islamic Rule in Southeast Asia

It was only in the late 18th and 19th centuries that Britain in Malaya, Thailand in 

the north, and the Dutch and the Spaniards in the archipelago began to embark on 

those competing and centralizing policies that led to the formation of the large political 

entities that today we call Malaysia, Thailand, Indonesia, and the Philippines. Prior 

to this time, the Islamic states in the region continued to survive, expand in number, 

engage in trade, and participate in shifting alliances that included relationships with 

the European companies designed to augment the regional strength of each. In the end, 

however, it was the English, Thais, Dutch, and Spaniards that prevailed, and as they 

did so Islam as a political force in the region was gradually disenfranchised. Although 

the pattern of imperial rule over the increasingly Muslim archipelago differed in 

each case, Islamic political authority was gradually ended. At the beginning of the 

20th century, only the sultans in the southern Philippines still claimed any degree of 

independent political authority, and their status was soon ended by American colonial 

policy in the Philippines.

As elsewhere in the Islamic world during this era, the collapse or co-opting of 

Islamic political authority by the prevailing imperial power left religious leadership 

in the hands of the `ulama, who no longer had the benefi t of a protecting political 

leadership. As Robert Hefner has noted in his brilliant study on Islam in Indonesia: 

Foreign control of the state led Muslim leaders to develop a cautious and 

critical attitude toward government, and forced them to rely on their own 

resources to develop their institutions... The tendency was for Muslim 

institutions to distance themselves from the state by locating themselves 

deep in native society. In Java and other areas of the archipelago, for 

example, the eighteenth and nineteenth centuries saw the spread of a 

vigorous little institution known as the pesantren, a Javanese variant 

of the...Qur’anic school...their educational function was made all the 

more important by state hostility toward Islam. [The] pesantren were 

also important because they provided a translocal network for native 

authority apart from the state.658

What was true in Indonesia was at least partially true in the rest of the Muslim 

archipelago. Lacking judicial institutions in which to apply Islamic law as qadis or 

a seat at the Sultan’s court as muftis to advise the ruler on aspects of Islamic law, 

the `ulama focused on the one role that remained available to them, their traditional 

educational role of imparting Islam and its requirements to the young generation of 

Muslims and advising the local community as required. The message they tended to 

impart, however, was that true political authority lay not with the colonial masters, but 

with God Himself whose will could be known in the absence of true political authority 

658 Robert W. Hefner, Civil Islam: Muslims and Democratization in Indonesia (Princeton, NJ: Princeton 

University Press, 2000), 33 – 34.
238

only by consultation with themselves. Under their tutelage, Islam increasingly became 

an authority structure outside of and apart from the state that tended to manifest itself 

as sullen, and unwilling, acquiescence to foreign ruling authorities, be it the Thai, 

British, Dutch, American, or Philippine ruling establishments.

Origins of the New Ruling Class

At the same time, however, the ruling colonial authorities embarked on educational 

programs of their own, designed to prepare a class of civil servants capable of assisting 

them in providing effective administration to the states they ruled. These programs, 

which often involved schooling in the home country or capital, tended to co-opt mainly 

the traditional ruling class associated with the historic ruling families (sultans/rajas) 

of the archipelago. As Indonesia and Malaysia began to move toward independence 

during and after World War II, it was individuals of this class who were best positioned 

to lead the movement toward independence, to bargain with the imperial authorities, 

and to lead their new countries in the modern international environment. Such leaders 

as the Cambridge-trained Tunku Abdul Rahman of Malaysia or the Dutch-educated 

Ahmad Sukarno of Indonesia, as well as their key associates, had a far different vision 

for the states they inherited than the far larger number of pondok- and pesantreneducated individuals who also had to be included in the new democratic institutions 

adopted by the newly independent states. Confl ict between these two competing visions 

of what independence from foreign rule should mean was inevitable and has been 

characteristic of the politics of both Malaysia and Indonesia since independence.

Malaysia

In Malaysia, the confl ict between the more modern, secular, and cosmopolitan 

leadership and those who envisioned a return of a more traditional Islamic political 

order has been muted by the perceived need to maintain Malay-Muslim unity in 

the face of the large non-Malay Chinese and Indian population that also inhabits 

the country. UMNO and the Barisan Nasional (National Front) that has dominated 

Malaysian politics from the beginning has been the primary vehicle for maintaining 

this unity. PAS, the party representing the more traditional vision within the Malay 

community, makes a strong showing in the northern and eastern, more nearly all-Malay 

states, but has failed to have strong appeal at the federal level and especially among 

the non-Malay communities. The aggressive and on the whole successful economic 

policies of the UMNO leadership over the years has also tended to co-opt the Islamist 

opposition, as has the adoption of a number of administrative procedures designed 

to make Malaysia appear more Islamic in character. The success of the UMNO in 

dominating Malaysian politics since independence in 1957, however, has also given 

Malaysia the appearance of being a one-party state that governs in a too authoritarian 

manner. Closely linked with the traditional ruling families that have governed the 

Malay peninsula for centuries, UMNO represents continuity with the past as well as 

change in response to the demands of modernity. Yet beneath the surface lies a level of 
239

dissent with the rather high-handed methods of the ruling party. Such dissent, of which 

the Islamic opposition is a part, tends to keep Malaysian politics in turmoil and keeps 

alive the prospect that political change of a quite radical nature is not unthinkable at 

some point in the country’s future.

Indonesia

In Indonesia, the confl ict between the two competing visions-the secular nationalist 

vs. the Islamic-has been present from the beginning. The Darul Islam movement that 

envisioned independent Indonesia as an Islamic state and competed with nationalist 

leader, Ahmad Sukarno, for leadership in the country’s war for independence (1945-

1950) was only the military vanguard of a much larger Islamic movement embodied in 

the Masjumi party. This party, which grouped together Indonesia’s two largest Islamic 

mass organizations — the modernist Muhammadiyah movement and the traditionalist 

Nahdlatul Ulama — competed for ascendancy in the newly independent country’s 

democratic institutions. Fully expecting to win Indonesia’s fi rst parliamentary elections 

in 1955, the party hoped to use electoral victory to achieve what military action had 

not.659 That they did not enabled Sukarno, leader of the Nationalist Party (PNI), in 

alliance with other secular parties, but particularly the Communist Party (PKI), to 

consolidate his nationalist agenda for the country. Sukarno’s growing reliance on the 

Communist party tended only to empower this group that also had rapidly growing 

support in Indonesia. With Sukarno’s support, the communists behaved ever more 

aggressively, polarizing Indonesian politics even further.

The denouement came in 1965, when an army coup d’état led by General Ahmad 

Suharto put an end to the Sukarno regime and the communist movement in Indonesia. 

Suharto’s action was not carried out on behalf of the Islamist factions of Indonesian 

politics, however, although he at fi rst had their active support. Rather, Suharto, using 

the army as his political base, sought to put an end to the anarchy he believed had 

characterized Indonesian democratic politics during the Sukarno era by constructing a 

strong, authoritarian state dominated by his own personal rule. As Benedict Anderson 

put it, Suharto’s policy was to make the state triumph over “society and nation.’’660

Suharto succeeded by suppressing both the Islamic and secular-nationalist wings of 

Indonesian politics, forcing them to merge into two competing political parties, the 

Islamic PPP and the secular-nationalist PDI, which he successfully sought to dominate 

through the construction of his own political party, Golkar, of which all government 

employees— military and civilian— had to be members. Meanwhile, paying lip service 

659 The Nahdlatul Ulama had withdrawn from the Masjumi in 1952 and therefore ran as a separate 

party in the 1955 elections, gaining 18.4 percent of the parliamentary vote as opposed to 20.9 percent for 

Masjumi. Together, the two were still considered the Islamic party in Indonesian politics at the time, but 

their combined vote of 39.3 percent was insuffi cient to give them control of the parliament. M.C. Rieklefs, 

A History of Modern Indonesia Since c 1200 (Stanford, CA: Stanford University Press, 2001), 298, 304.

660 Benedict R. O’G. Anderson, “Old State, New Society: Indonesia’s New Order in Comparative 

Historical Perspective,” in Benedict R. O’C. Anderson, ed., Language and Power: Exploring Political 

Cultures in Indonesia (Ithaca, NY: Cornell University Press, 1972), 109.
240

to capitalism as the basis of the country’s economy, Suharto also placed emphasis 

on state-owned corporations as the primary means to facilitate Indonesia’s economic 

development, thus transforming the employees of most of the country’s engines of 

economic growth into civil servants who also had to be members of Golkar.

For more than three decades, Suharto’s étatist policies worked, gradually 

transforming Indonesia into a dynamic economic powerhouse in Southeast Asia. With 

this transformation, however, came other changes, most notably the growth of an 

increasingly large, better-educated middle class that was increasingly less enchanted 

with the corrupt and authoritarian nature of the Indonesian state. Closely associated 

with this change was the nearly simultaneous emergence of what Robert Hefner has 

called “civil Islam.’’ Articulated by a body of new intellectuals, the most notable 

of which was Nucholish Madjid, this school of thought argued that Muslims were 

wrong to work for the establishment of an Islamic state and in fact diminished the 

“high values’’ of Islam when they did so. Rather, Muslims should work to ensure that 

the high values of Islam were refl ected in the state as well as the society, and such 

values did not support the corruption, cronyism, brutality, and authoritarianism of the 

current state.661 Such an argument that accepted the political disenfranchisement of 

Islam was in fact encouraged by the Suharto government and found resonance in the 

newly emerging middle class, which underwent a general process of “santrifi cation’’ 

(becoming more conscious of Islamic observance) during this same era.

So powerful did the movement become that, by the 1990s, Suharto decided 

to bestow his favor on it by authorizing the establishment of the Association of 

Indonesian Muslim Intellectuals (ICMI). His offi cial support of this Islamic movement 

was not intended to empower it, however, as much as to control it and ensure that it 

did not join forces with other groups in Indonesian society seeking to end his system 

of authoritarian rule.662 He might have succeeded in this ploy had it not been for the 

Asian fi nancial crisis of 1997, which seriously undermined his control of Indonesian 

politics and led to his resignation in May 1998 in the face of a united opposition that 

joined the proponents of civil Islam and the secular nationalists in a popular movement 

to restore true democratic rule in Indonesia.

With the election of Islamic reformist leader Abdurrahman Wahid, a proponent of 

civil Islam, as President of Indonesia in October 1999, it appeared that the authoritarian 

New Order regime of Ahmad Suharto was fi nally over, and forces favoring change 

solely on a democratic basis had achieved ascendancy. As Robert Hefner has noted, 

“the proponents of civil Islam” were “a key part of this renaissance,” and proponents 

of “statist Islam” had become a minority.663 For the moment, at least, those elements 

favoring radical political change, be it from the left or from the Islamic right, have 

been marginalized, despite efforts of the militant Islamist group, Jemaah Islamiyah, 

661 Hefner, Civil Islam, 116 – 119.

662 Hefner, Civil Islam, 129.

663 Hefner, Civil Islam, 218.
241

to make its presence felt and to influence public opinion by continued periodic 

terrorist operations.

Thailand and the Southern Philippines

The situation of the Malay Muslim populations of southern Thailand and the 

southern Philippines was far more bleak. Unlike the inhabitants of Malaysia and 

Indonesia, those “colonial powers’’ which had come to dominate them politically were 

not distant European powers for whom colonialism was no longer fashionable nor 

profi table. Their “occupiers’’ were nearby regimes who considered the territories they 

inhabited integral parts of the nation state of which they were a part. Despite being the 

inheritors of proud local histories, they had become “indigenous minorities’’ of rapidly 

modernizing states of which most did not wish to remain a part. A result of this cultural 

alienation has been, since the 1960s in the case of southern Thailand and the 1970s in 

the case of the southern Philippines, long-term insurgencies aimed at demonstrating 

to the ruling governments the diffi culty of ruling a restive population that rejects the 

authority of “foreign’’ rule.

During the earlier phase of these insurgencies, the “national’’ character of the insurgent 

movement — Malay in southern Thailand and Moro in the southern Philippines — was 

stressed. Since the late 1980s and 1990s, however, the “nationalist’’ appeal has given 

way to a more Islamist appeal in both cases. In the southern Philippines, the MILF has 

become the principal source of resistance to the central government rather than the 

MNLF, and in southern Thailand the secretive GMIP appears to have replaced PULO 

as the most active agent of the continuing insurgency. The change certainly refl ects 

the general Islamic resurgence that has been apparent throughout the Islamic world 

since the 1970s, but more specifi cally it refl ects the inspiration of the successful jihad

conducted by the Afghan resistance against the Soviet occupation of that country in 

the 1980s.

Western and other international supports of the Afghan resistance to the Soviet 

occupation of Afghanistan may or may not have perceived that their support was 

empowering a jihad movement. To those who were actually engaged in the combat, 

however, but especially the foreign fi ghters who came to lend their support, it was 

indeed a jihad, a sanctifi ed and holy resistance movement against an infi del whose 

power seemed irresistible.664 The success of the Afghan jihad in leading one of the 

two major global superpowers of the day to reverse its course and withdraw from 

Afghanistan raised hopes among Muslim minorities throughout the world, including 

those in southern Thailand and the southern Philippines. If one of the major superpowers 

664 In fact, for the Afghans themselves, it is uncertain that many perceived their resistance as a holy war 

for Islam. Many simply saw the confl ict as a national resistance movement against a foreign occupier. The 

foreign fi ghters involved, to include the Pakistani government of Zia al-Haq, as well as some of the more 

radical Afghan groups, justifi ed their involvement on a religious basis, that is, they were engaged in a jihad

that was larger than the Afghan confl ict and would not necessarily end after the Soviet withdrawal.
242

could be forced to lift its occupation, then perhaps it was possible for the governments 

of Thailand and the Philippines to reach a similar conclusion.

Statist Islam vs. Civil Islam

Unlike Indonesia and to some degree Malaysia as well, where “statist Islam,’’ 

to use Robert Hefner’s terminology, has been and continues to be effectively 

marginalized politically, in southern Thailand and the southern Philippines, it appears 

to be ascendant. As far as we know, the goal of both the GMIP and the MILF is to 

achieve the independence of the Muslim peoples, whom they claim to represent, by 

the establishment of an “Islamic state.’’ In support of this objective, they have had 

at least a degree of support from two other clandestine organizations-the globallyoriented al-Qa'ida movement, established by Usama bin Ladin in Afghanistan in 1988, 

and the regionally-oriented Jemaah Islamiyah movement founded by the Indonesians 

Abdullah Sungkar and Abu Bakar Ba’asyir in Malaysia in 1993. Although the 

leadership of Jemaah Islamiyah from the beginning had a fundamentally Indonesian 

orientation, which became readily apparent after the fall of Suharto in 1998, it began 

as an organization having a regional objective of facilitating the transformation of the 

whole Muslim archipelago that has been the focus of this study into an Islamic state. 

The formation of Jemaah Islamiyah appears to have been a result of meetings between 

bin Ladin and the two Indonesian clerics in Pakistan in 1991. The organization had 

diffi culty maintaining focus on the larger regional perspective after the fall of Suharto, 

however. It nevertheless continued to pose a terrorist threat in Indonesia until at least 

2005. The Abu Sayyaf Group (ASG) in the southern Philippines appears to have 

originated as a unique group having ties primarily to al-Qa'ida. No evidence has been 

uncovered during this research of linkages between the ASG and Jemaah Islamiyah.

Islam, whether in its more modern civil variety or the more traditional statist version, 

has played and will continue to play a signifi cant role in the politics of Southeast Asia. 

The traditional view that religion and politics are inseparable in Islam, repeatedly 

articulated over the centuries by traditional Islamic scholars from Ibn Taymiyya to 

Sa`id Qutb still holds sway over the minds of many Muslims around the world. In this 

view, there can be no security for Islam or the Muslim peoples without the protection 

of an Islamic state, one in which Islamic law (shari`a) is the law of the land and is 

effectively administered by competent authorities. Unfortunately, the former western 

colonial powers as well as the current Thai and Philippine governments have done 

little to disabuse the Muslims of Southeast Asia of this view.

As Robert Hefner has noted, however, we all — Muslims included — live in a 

complex, modern world that is characterized by “migration, urbanizations, and 

communications that render borders permeable to transcultural fl ows.’’ In such a world, 

“the markets, media and migrations...make any enduring institutionalization of...statist 

Islam diffi cult...The arrangement fails because it is so out of step with the pluralism 
243

and movement of our age.665 In today’s globalized marketplace of ideas, opinions 

and sources of information come from many sources. Every idea is challenged, 

and ultimate truth is elusive. In the end, Muslims may fi nd, as they apparently are 

fi nding in Indonesia, that the high values of Islam are more effectively maintained in 

an environment in which freedom of religion is guaranteed rather than one in which 

religion is coerced.

665 Hefner, Civil Islam, 219 – 220.

245

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265

JOURNALS

Annual Review of the Social Sciences of Religion

Asian and African Studies (Israel)

Asian Studies Review

Asian Survey

Asian Thought and Society

Asia-Pacifi c Review

Australian Journal of International Affairs

Confl ict

Contemporary Southeast Asia

Far Eastern Economic Review

Indonesia

Inside Indonesia

Jane’s Intelligence Review

Journal of Asian and African Studies

Journal of Asian Studies

Journal [of the] Institute of Muslim Minority Affairs

Journal of Southeast Asian Studies

Muslim World

Nationalism and Ethnic Politics

Sojourn

Studia Islamika

Survival

Terrorism and Political Violence

Third World Quarterly 

267

A

Abduh, Muhammad 16, 49, 99

Abdul Kadir, Tengku 64

Abdul Rahman, Kabir 69

Abdul Rahman, Tunku 16, 32, 238

Abhangen 24, 25, 26, 85, 86, 99, 113

ABIM (Angkatan Belia Islam Malaysia—Malaysian Islamic Youth Movement)

 v, 38, 39, 40, 41, 43, 71, 91

Abu Jibril (Muhammad Iqbal Rahman) 47

Abu Zubayda 105, 131, 209

Aceh vii, 166, 167, 168, 190, 259, 267, 268, 270

Act of Free Choice 141

Afable, Silvestre 223

Ahtisaari, Martii 166

Al-Azhar University (Cairo) 182, 187, 195

Al-Ma’unah 53

al-Mukmin 48, 49

Alonto, Datu Abulkhayr 188, 226, 263

Al-Qa’ida v, ix, 3, 46, 47, 48, 50, 51, 52, 54, 74, 76, 82, 103, 104, 105, 106,

 107, 108, 114, 129, 131, 133, 136, 137, 160, 162, 197, 201, 203, 204,

 205, 208, 209, 210, 211, 212, 219, 242

Ambon 117, 123, 124, 125, 126, 127, 129, 138

AMCJA (All-Malayan Council of Joint Action) 15 

AMM (Aceh Monitoring Mission) 166, 167

Ancestral Domain 225, 228

Anglo-Siamese Treaty of 1909 62

Aquino, Agapito 200

Aquino, Benigno 186, 199

Aquino, Corazon (President of the Philippines, 1986-1992) 193, 199, 202,

 203, 204, 205, 207

Arismanandar 132

ARMM (Autonomous Region of Muslim Mindanao) 207, 208, 209, 212, 216,

 217, 218, 219, 227

Arroyo, Gloria Macapagal (President of the Philippines, 2001- ) 215, 216,

 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230

ASG (Abu Sayyaf Group) 103, 108, 203, 204, 205, 206, 207, 208, 209, 211,

 212, 213, 215, 216, 217, 218, 219, 220, 222, 223, 226, 242

Asian Financial Crisis 42

Atef, Muhammad 50, 103, 160, 205

Autonomous Region 192, 193, 194, 195, 198, 200, 202, 206, 207

INDEX
268

Aziz, Nik Adli Nik 41, 50, 53

Azzam, Abdullah 46, 47, 102

Azzarouk, Rajab 212

B

Badawi, Abdullah Ahmad 55, 56, 80

Bahasa Indonesia 2, 100, 119, 268

Bahasa Malaysia 2, 16, 268

Bali bombing, (October 12, 2002) 139, 140, 168, 221

Banda Aceh 159, 164

Bangkok 60, 63, 66, 70, 76, 78, 156

Banna, Hasan al- 99, 100

Bantam 5

Barisan Alternatif 44

Barisan Nasional (National Front) 32, 37, 40, 41, 44, 56, 70, 74, 238

Basilan 204, 205, 211, 213, 218, 219, 220, 226

Batavia 10, 19, 21, 22, 23, 26, 59, 236

Bates, General John C. 172

BDA (Bangsamoro Development Agency) 228

Belo, Bishop Carlos Filipe Ximenes 120

Bersatu (Solidarity) 74

Beureueh, Daud 151

Biel, Luis “Ton-ton” 204

Bin Ladin, `Usama 3, 47, 48, 76, 77, 103, 106, 126, 129, 196, 197, 201, 205,

 209, 219, 242

Black December (1902) 71

BMLO (Bangsa Moro Liberation Organization) 192, 193

BNB (Barisan Nasional Baru) 74

BNPP (Barisan Nasional Pembebasan) 71

Borneo 13, 18, 50, 107, 124, 133, 171, 209

Borobodar 98

BPUPKI (Badan Penyelidik Usaha Persiapan Kemerdekaan Indonesia) 

 3, 26

Bravo, Commander (alias for Abdullah Macaapar) 213

BRN (Barisan Revolusi Nasional—National Revolutionary Front) 68, 69, 70,

 77, 82

Brooke, James 13

Brunei 1, 2, 5, 9, 13, 18, 50, 76, 107, 141, 154, 209, 225

Budi Utomo 23

Buliok Complex 222, 224

Bupati 20, 22
269

Burma 11, 61, 62, 64, 65, 76, 80

Burnham, Gracia 218, 220, 223

Burnham, Martin 218

Bush, President George W. 54, 114, 116, 162, 219, 220, 223, 225

C 

Caday, Leonides 214

Cambodia 1, 2, 3, 7, 62, 64, 119, 160

Camp Abu Bakar 133, 135, 201, 202, 208, 209, 213, 214, 215, 222

Camp Hudaibiyah 105, 107, 133, 139, 209, 210, 213, 214

Camp John Mack 213

Camp Saadah 101, 102

Camp Shafi `I 203, 209

Carpenter, Frank 176

Cham 1, 2, 3, 7

Chulalongkorn (Rama V), King of Siam (1868-1910) 11, 61, 62

CMI (Crisis Management Initiative) 166

CNI (Committee on National Integration) 182

Cokroaminoto, Haji Umar Said 23

Corpus, Victor 223

Cotabato 192, 193, 194, 195, 198, 200, 201, 202, 208, 210, 213, 222

CPM (Communist Party of Malaysia) 15, 31, 68, 69, 78

Crown Colony 11, 13, 15

Cultivation System 20, 21

D

DAP (Democratic Action Party) 41

Darul Arqam 34, 35, 36, 37, 38, 46, 73

Darul Islam v, 4, 28, 48, 49, 53, 86, 87, 90, 95, 96, 97, 99, 100, 102, 131, 151,

 152, 153, 155, 168, 197, 239

Datu 173, 174, 181, 184, 185, 188, 191, 192, 194, 195, 198, 200

Davao 192, 193, 204, 222, 225, 226

DDII (Dewan Dakwah Islamiyah Indonesia) 93, 94, 95, 97, 99, 101, 128,

 132

Dekker, Dowes (Danudirja Setyabuddhi) 23

Demak 5

Di Tiro, Hasan 155, 156, 159

Di Tiro, Teungu Chik Maat 155

Dili 120, 121

DOM (daerah operasi militer) 157, 158

Dos Palmos 220

Dutch East Indies 10, 11, 20, 21, 22, 23, 25, 62, 63, 118, 153
270

Dwikarna, Agus 136, 160

E

East India Company 10, 11, 13, 19, 60

EDCOR (Economic Development Corps) 180

Eluay, Theys Hiyo 144, 146

England/Great Britain 9, 10, 11, 62, 175

Ermita, Edwardo 223

Estrada, Joseph (President of the Philippines, 1998-2001) 211, 212, 213, 215

Ethical Policy 22, 23

F

Fadillah, Haris (aka Abu Dzar) 131, 132

Farouk, Omar al- 105, 131, 136, 160, 209

Federation of Malay States (Malay Federation) 12, 13, 14, 64, 65

Federation of Malaysia 15

Foreri (Forum for the Reconciliation of Irian Jaya Society) 144, 147

FPI (Front Pembala Islam—Islamic Defenders Front) 167

Freeport-McMcRan Copper and Gold, Inc. 142, 143, 148

Fretilin 118, 119, 120, 142

G

GAM (Gerakan Aceh Merdaka—Free Aceh Movement) 151, 155, 156, 157,

 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168

General Santos City 214, 226

Gestapu coup 89, 95, 154

Ghamdi, Hemaid H. 51

Ghozi, Fathur Rahman al- 96, 108, 135, 214, 215, 226

GMIP (Gerakan Mujahideen Islam Pattani—Pattani Islamic Mujahideen 

Movement) 73, 74, 77, 82, 241, 242

Golkar (Golangan Karya) 81, 90, 92, 109, 110, 112, 115, 154, 165, 239, 240

Gusmao, Jose Alexeandre (aka “Xanana”) 120

H

Habibie, B.J. 93, 110, 111, 112, 144, 150, 157, 158, 159

Hambali (Riduan Isamuddin) 47, 48, 50, 51, 52, 76, 78, 107, 134, 135, 140,

 203, 215

Hamza, Tenku Razaleigh 41, 42, 113, 114

Hashim, Salamat 173, 185, 188, 192, 194, 196, 197, 198, 199, 200, 203, 208,

 210, 213, 214, 219, 221, 222, 224

Hatta, Muhammad 3, 23, 25, 26, 28, 153
271

Haz, Hamza 113, 114, 128

HDC (Henri Dunant Center for Humanitarian Dialogue) 162

Hekmatyar, Gulbuddin 195

HMI (Himpunan Mahasiswa Islam—Islam University Student Movement)

 90, 91

Horta, Jose Ramos 120

Huk (Hukbalahap) rebellion 179, 180, 186

Hussein, Parouk 216, 217, 227

I

Ibrahim, Anwar v, vi, 36, 38, 39, 40, 43, 44, 45, 54, 55, 56, 91, 205

Ibrahim, Ustaz 45

ICFM (Islamic Conference of Foreign Ministers) 187, 189

ICMI (Association of Muslim Intellectuals) 93, 111, 113, 240

IIRO (International Islamic Relief Organization) 201, 203

IMF (International Monetary Fund) 108, 109

IMT (International Monitoring Team) 227

Indies Party 23

INTERFET (U.N. International Force in East Timor) 121

Internal Security Act 41, 53

Ipil 204, 209

Irian Jaya (West New Guinea or Papua) 50, 88, 107, 117, 129, 141, 142, 145,

 146, 147, 150, 151, 153, 156, 160, 168

Isamuddin, Riduan, see Hambali

ISI/ISID (Inter-Services Intelligence Directorate, Pakistan) 196

Iskandar Muda 155

Islam Hadhari (Civilized Islam) 56

Ismail, Zainon 52, 53

Ittihad-i Islami 196

J

Jabida “massacre” 183

Jakarta 96, 98, 101, 108, 110, 113, 116, 123, 125, 126, 128, 129, 131, 139,

 140, 141, 143, 145, 151, 154, 156, 159, 162, 164, 168, 206, 207, 208,

 212, 214, 216, 217, 219

Jakarta Agreement 206, 207, 208, 212, 216, 217, 219

Jamaat Tabligh 34, 35, 36, 37, 38

Jamiyat-i Islami (Pakistan) 36, 39, 196

Janjalani, Abdurajak 48, 196, 197, 200, 203, 204, 205, 211

Janjalani, Khaddafy 211, 220, 221, 222, 226, 227

Japan (World War II) 3, 64, 65, 87, 175
272

Java 4, 5, 7, 8, 10, 19, 20, 21, 22, 23, 24, 26, 27, 28, 48, 61, 85, 87, 88, 94, 95,

 97, 107, 123, 126, 133, 140, 152, 153, 154, 155, 156, 236

Java War (1825-1830) 19, 20

Jogjakarta (see Yogjakarta)

Johore 5, 10, 11, 14, 17

Jolo 171, 188, 189, 191, 217, 221, 226, 227

K

Kalimantan 4, 50, 107, 108, 117, 124, 133

Kalla, Yusef 138, 164, 165, 167

Kartosuwiryo, Soekarmadji 87

Kebatinan 85

Kedah 10, 11, 14, 16, 17, 37, 44, 45, 59, 60, 62, 65, 67

Khalifa, Muhammad Jamal 48, 201, 203

Khomeini, Ruhollah 100, 104

Kiram II, Jamal al-, Sultan of Sulu 172, 191

Kiram, Datu Mahakutta, Sultan of Sulu 191

KISDI (Committee for Islamic Global Solidarity) 128

Kittikachorn, Thanom 71

KMM (Kampalan Mujahidin Malaysia) 52, 53, 54, 56, 57, 58

Komando Jihad 96, 97, 155

Konsojaya Trading Company 51

Kopassus 147, 148, 149

Kota Baru 40, 51, 52

Krue Se mosque 79

Kuala Lumpur 6, 12, 15, 18, 32, 35, 36, 37, 45, 52, 53, 54, 107, 216, 219, 224,

 225, 226, 228

L

Laskar Jihad 123, 125, 126, 127, 128, 129, 131, 132, 133, 137, 138, 140, 145,

 149, 150, 167

Laskar Jundallah 136, 138, 160

Laskar Mujahidin 125, 129, 131, 132, 134, 167

Lhokseume 158, 160, 161

Liberal Policy 21, 22

Libya 70, 182, 187, 188, 190, 195, 205, 212

Loncar, Badimir 162

Lucman, Datu Rashid 185, 192

M

Macapagal, Diosdado (President of the Philippines, 1961-1965) 18, 215

Madjid, Nurcholish v, 91, 113, 240
273

Mahmud, Malik 167

Mahyiddeen, Tenku Mahmud 64

Makaram, MGEN Zacky Anwar 121

Makassar (Ujung Pandang) 5, 108, 126, 136, 138, 165

Maktab al-Khidmat (Services Bureau) 46, 102

Malaca 5, 7, 8, 9, 10, 11, 15, 18, 39, 48, 49, 56, 59, 61, 236

Malayan Union 15, 16, 31

Malik, Habier 227

Malino Declaration 138

Malino II Agreement 138

Manila 6, 9, 10, 18, 135, 171, 173, 175, 177, 179, 180, 181, 182, 183, 184,

 188, 191, 198, 201, 205, 206, 208, 214, 215, 217, 220, 221, 223, 225,

 226, 227, 228, 229, 230

Manuputty, Alexander 128

Marcos, Ferdinand (President of the Philippines, 1965-1986) 46, 171, 183,

 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 195, 197, 198, 200,

 202, 205, 207

Masduki, Ajengan 102

Masjumi/Masyumi (Majlis Syura Muslimin Indonesia) 86, 87, 88, 89, 90, 93,

 94, 97, 239 

Mat, Nik Aziz Nik 41, 52

Matalam, Datu Udtag 184

Mataram 5

Matha, Wan Muhammad Noor 67, 71

MCA (Malaysian Chinese Association) 16, 31, 32, 41

MCP (Malaysian Communist Party) 15

Medina, University of (Saudi Arabia) 182

Memali Commune 46

MIC (Malaysian Indian Congress) 16, 31, 32

MIM (Muslim/Mindanao Independence Movement) 184, 187

Minangkabau 5

Misuari, Nur 184, 185, 188, 190, 192, 193, 194, 195, 199, 200, 202, 206, 207,

 212, 216, 217, 227

MMI (Majelis Mujahidin Indonesia—Congress of Indonesian Mujahidin)

 134, 136, 140

Mohammad, Mahathir 55, 74, 92, 157, 171, 216, 223, 227

MTCP (Malaysian Technical Cooperation Program) 228

MTF (Mindanao Trust Fund) 228

Muhammadiyah 23, 24, 25, 49, 86, 89, 94, 98, 99, 112, 125

Mujahidin KOMPAK (Komite Aks Penanggulangan Akibat Krisis—Action

 Committee for Crisis Response) 132, 136

Mukhlus (alias for Ali Gufron) 107, 134

Murad, Abdul Hakim 203, 205
274

Murad, Haj Ali 185, 197, 200, 203, 213, 224

Murtopo, General Ali 95, 96

Muslim Brotherhood (Al-Ikhwan al-Muslimin—Egypt) 24, 36, 99, 100

Mustafa, Tun 185, 190

N

Nahdlatul Ulama 24, 25, 86, 89, 98, 113, 239

NAM (Non-Aligned Movement) 40, 153

Narathiwat 2, 59, 67, 68, 77, 78, 79, 80

Nasution, Abdul Haris 153

Natsir, Muhammad 93, 94, 97

Negeri Sembilan 11, 17, 35, 50

NEP (New Economic Policy) 32, 33, 36, 38, 43

New York Agreement 141, 142

Ngruki, Pondok 48, 96, 97, 100, 101, 102, 131, 132, 134, 135

NLSA (National Land Settlement Administration) 177

NOC (National Operations Council) 32

North Borneo Company 13

NPA (New People’s Army) 186, 199, 200, 223, 228

O

OIC (Organization of the Islamic Conference) 40, 187, 189, 190, 191, 192,

 193, 194, 198, 200, 200, 207, 216, 217, 224, 225, 227

Onn, Dato Hussein 16, 37, 39

Operation ENDURING FREEDOM 220

OPLAN Bojinka 51, 103, 106, 107, 108

OPM (Organisasi Papua Merdaka—Free Papua Organization) 142, 144, 147,

 148

P

Pancasila vii, 3, 86, 90, 91, 93, 95, 98, 99, 112, 114, 119, 120, 151, 167, 169

PAP (People’s Action Party) 17

Papua, see Irian Jaya 

Paramesawar (Megat Iskander Shah) 5

PAS (Parti Islam seMalaysia) v, 36, 37, 38, 39, 40, 41, 44, 45, 52, 53, 54, 55,

 56, 70, 74, 80, 238

Patronage of Islam Act 65

PDI (Indonesian Democratic Party) 89, 239

PDI-P (Indonesian Democratic Party for Struggle) 112, 114, 115

Penang 10, 11, 15, 18, 60

Pendola 137, 139

Perak 5, 11, 17, 35, 44, 53, 107
275

Perlis 11, 14, 17, 44, 60, 62, 64, 65

Pesantren 7, 25, 48, 97, 101, 102, 107, 136, 237

Phibun (Field Marshal Luang Plaek Phibunsonkhram) 64

Philippine Constabulary 176, 177, 205, 206, 211

PII (Pelajar Islam Indonesia—Islamic Student Movement) 90

Pitsuwan, Surin 59, 67, 71, 162

PKI (Communist Party of Indonesia) 24, 87, 88, 89, 239

PLO (Palestine Liberation Organization) 70, 183

PMI (Partai Muslimin Indonesia/Parmesi—Indonesian Muslim Party) 89, 90

PNI (Nationalist Party of Indonesia) 25, 239

Pondok 7, 61, 67, 68, 97, 98, 100, 101, 102, 107, 131, 132, 134, 238

Portugal 8, 9, 118

PPP (United Development Party) 89, 90, 96, 112, 113, 114, 115, 128, 239

Priyayi 20, 22, 23, 26, 85

PULA (Pattani United Liberation Army) 70

PULO (Pattani United Liberation Front) 69, 70, 71, 74, 76, 77, 83, 155, 157,

 183, 241

PUPJI (Pedoman Umum Perjuangan al-Jamaah al-Islamiyah) 47, 104, 105,

 106, 107, 138

Q

Qadhafi , Mu’ammar 157, 185, 186, 188, 216

R

Rabbani, Burhanuddin 195

Rabitat al-`Alam al-Islami (Islamic World League) 94

Raffl es, Thomas Stamford 10

Rahman, Muhammad Iqbal, (see Abu Jibril) 47, 50

Rais, Amien 91, 112, 125

Ramos, Fidel (President of the Philippines, 1992-1998) 205, 206, 207, 208,

 210, 211, 213, 216, 230

Raya Indonesia 3, 18

Razali, Mohammad Amin 53

Resident System 12

Reyes, General Angelo 223

Rida, Rashid 23, 49, 99

Robot, Commander (alias for Galib Andang) 211, 226

RSM (Republic of South Moluccas) 123, 128

Ryncuda, General Ryamizard 165
276

S

Sabah 8, 13, 18, 19, 41, 50, 107, 139, 171, 183, 185, 187, 189, 190, 197, 209,

 212, 217

Sabil-illah 71

Saesaeng, Nasori (“Sori”—alias for Wae Ka Raeh) 73

Samudra, Imam (alias for Abdul Aziz) 194, 134, 140

Sandakan 139

Santa Cruz “massacre” 120

Santri 24, 25, 26, 85, 86, 89, 99

Sarawak 8, 13, 18, 19, 50, 107, 209

Sarekat Islam 23

Sayyaf, Abd al-Rasul 102, 196

SBPAC (Southern Border Provinces Administration Center) 71, 75

SBPPBC (Southern Border Provinces Peace Building Command) 78

Sedition Act of 1948 32

Selangor 11, 17, 35, 107

Shah, Wali Khan Amin 51, 203

Shari`a 90, 99, 100, 112, 114, 153, 167, 168, 169, 173, 176, 181, 209, 233,

 236, 242

Shinawatra, Thaksin 75, 80

Singapore 1, 10, 11, 15, 17, 18, 19, 38, 46, 50, 66, 69, 76, 85, 90, 102, 103,

 104, 106, 107, 108, 114, 131, 135, 185, 209

Sipidan Island 212, 213, 215, 217, 218

 Referendum on Aceh) 159

Solana, Javier 212

Solo (Surakarta) 48, 97, 101, 108, 132, 134

Solossa, Jacobus (“Japp”) 148

Spain 8, 9, 13, 171, 172, 175

SPCPD (Southern Philippines Council for Peace and Development) 206, 207,

 216

Strait of Malacca 10, 48, 56

Sufi sm 7, 235, 236

Suharto, Ahmad 19, 43, 46, 47, 49, 50, 89, 90-124, 131-135, 141-144, 151,

 154-158, 165-168, 210, 239-242

Sukarno, Ahmed vii, 3, 18, 19, 23-28, 37, 48, 86-90, 93, 110, 112, 141, 152-

 154, 162, 238, 239

Sukarnoputri, Megawati 112, 113, 128, 146, 150, 161, 164

Sulu 6, 9, 10, 13, 18, 108, 171-175, 180-185, 188-193, 199, 202-204, 211,

 212, 22-222, 226

SIRA (Sentral Informasi Referendum Aceh—Information Center for a
277

Sumatra 4, 5, 6, 10, 20-24, 27, 28, 56, 59, 89, 105, 107, 135, 151-155, 190,

 236 

Sungei Manggis 48

Surabaya, Battle of 26, 97, 108, 126

Syria x, 70, 182

T

Tanjung Priok “massacre” 98

Tantra Jihad Islam 74

Ternate 9, 123

Terengganu 11, 14, 17, 37, 44, 55, 60, 64, 65, 105

Thalib, Jaffar Umar 125-129, 137, 149

Tibo, Fabious 136, 137

TMSA (Thai Muslim Student Association) 71

Tobelo “massacre” 125

Tripoli Agreement 190-194, 197, 198, 206, 219, 228, 229

TRT (Thai Rak Thai) 80

Tsunami 164-167, 190

U

UMNO (United Malays National Organization) 15, 16, 31-56, 70, 80, 81,

 238

United East India Company 10, 19

UNTAET (U.N. Transitional Administration for East Timor) 121

USIP (United States Institute of Peace) 225

Usroh 99, 100

USS Cole, Bombing of 51, 52

V

Vietnam 1, 2, 3, 6, 7, 26, 34, 62, 80, 81, 119, 133

W

Wahid, Abdurrahman (Gus Dur) 91, 112, 113, 114, 126, 127, 128, 144, 145,

 147, 150, 159, 161, 240

Wirajuda, Hasan 160

Wiranto, General 110, 158

World Bank 228

Y

Yala 2, 59, 61, 67, 73, 75, 76, 77, 78, 80

Yang di-Pertuan Agong 16, 17
278

Yap, Edilborah 218

Yogjakarta 21, 23, 27, 126, 135

Yousef, Ramzi 48, 51, 103, 203, 205, 210, 211

Yunos, Mukhlis 214, 215

Z

Zamboanga 191, 192, 193, 204, 217, 218, 220, 221

Zia al-Haq 241

Zinni, Anthony 162

Zulkarnaen 132
PCN 5160

ISBN 978-1-932946-19-2