The Mindanao 

Peace Talks 

Another Opportunity to Resolve 

the Moro Conflict in the Philippines

Summary

• The stalemate between the Philippine government and the insurgent forces of the 

Moro Islamic Liberation Front (MILF), the ongoing global War on Terror, and the 

government’s desire for peace in the southern Philippines in order to bolster the 

country’s economy have created an environment conducive to a resolution of the 

Muslim secessionist rebellion in the south. A leadership change in the MILF has 

also provided an opportunity to reinvigorate and seek new approaches to the peace 

process. 

• The biggest obstacle in the peace process is no longer whether the parties can reach 

an agreement, but whether that agreement can really bring sustainable peace and 

development in the south. The long history of the conflict and the failed approaches 

to resolve it have created deep divisions among Muslims and among the general Filipino populace, which regards any peace agreements with skepticism or, at the most, 

guarded optimism. 

• The peace pact must be able to offer a detailed roadmap that directly addresses the 

grievances of Muslims in the Philippines. Yet that roadmap can significantly contribute to peace only when it is supported by the majority of Filipinos. The government 

and the MILF must reach out to their own constituencies and engage their active 

support of the peace process. President Gloria Macapagal-Arroyo must take an active 

personal role in winning over the hard-liners and in cultivating national backing. 

The government and the MILF must go beyond their narrow group interests to find 

workable solutions to the problems of the country’s Muslim minority. 

• To reach common ground, it is imperative that the parties explore all options for a 

political arrangement that can accommodate their conflicting interests. They must 

get out of the “independence-autonomy track” that has constricted past peace processes and explore different models and political structures that have worked well in 

settling secessionist conflicts elsewhere. 

www.usip.org

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SPECIAL REPORT 131 JANUARY 2005

ABOUT THE REPORT

The drawn-out peace talks that began in 1997 

between the Philippine government and the Moro 

Islamic Liberation Front (MILF) are entering a critical 

stage as negotiations on substantive aspects are 

scheduled to commence in February 2005 in Kuala 

Lumpur, Malaysia. An agreement with the MILF is 

an important piece in finding a solution to more 

than three decades of secessionist insurgency in the 

southern Philippines. A settlement will also boost 

global efforts to put a lid on the resurgence of Islamic 

extremism in Southeast Asia. This report explains the 

origins of the conflict, the evolution of the peace 

process, and the challenges facing both sides. It also 

recommends measures for a successful resolution. 

This is the first report from the Philippines Facilitation 

Project of the United States Institute of Peace. The 

report was written by Benedicto R. Bacani, dean of 

the College of Law, Notre Dame University in Cotabato 

City, Philippines, and currently a senior fellow in the 

Institute’s Jennings Randolph Program for International 

Peace. Bacani is completing a book on autonomy as a 

solution to violent conflicts, drawing on lessons from the 

experiences of the southern Philippines. 

UNITED STATES INSTITUTE OF PEACE

SPECIAL REPORT

The views expressed in this report do not necessarily reflect 

those of the United States Institute of Peace, which does 

not advocate specific policy positions.

CONTENTS

Introduction 2

Origins of the Conflict 3

Evolution of the Government– 

MILF Peace Process 5

Ripe for Resolution 7

Challenges in the Talks 8

Conclusion 11
• Any peace agreement must provide strong mechanisms for implementation. 

Peace processes in the past have produced good agreements but were poorly 

implemented. A neutral third party must be engaged to oversee the implementation 

of the peace pact. 

Introduction

The peace talks between the Philippine government and the Moro Islamic Liberation Front 

(MILF) that began in 1997 will enter the critical stage in February 2005 in Kuala Lumpur, 

Malaysia as the parties begin negotiations to arrive at a common understanding about the 

substantive issues of the conflict. This round is a milestone in a drawn-out peace process 

often derailed by allegations of the MILF’s links with terrorist organizations, two major 

wars, sporadic skirmishes, and charges and countercharges of violation of the cease-fire 

agreement forged by the parties on July 18, 1997. 

Both sides made concessions to get to this stage. Despite protests from hard-liners, 

the Philippine government repositioned its troops away from rebel strongholds and withdrew arrest warrants against the leaders of the MILF for alleged involvement in bombings 

throughout the country. For its part, the MILF provided information to neutralize groups 

engaged in kidnappings in an effort to disprove allegations of its links with terrorist 

organizations—particularly with Abu Sayyaf, a local terrorist group engaged in the widely 

publicized kidnappings of foreigners, and Jemaah Islamiyah.

The 9/11 terrorist attacks on the United States brought new prominence to the Islamic 

militancy in the Philippines, particularly in Mindanao, the country’s second largest island 

and the arena of the struggle for an independent Islamic state by the MILF. Reports of the 

separatist movement’s links with al Qaeda, Abu Sayyaf, and Jemaah Islamiya jolted the 

Philippine government into a frenzied search for a solution to its Muslim problem.1

The strategic importance of a peace accord between the government and the MILF 

cannot be overemphasized. Negotiating a workable settlement with the MILF is the last 

major piece in the puzzle for lasting peace in the southern Philippines. In 1996, Manila 

forged a peace agreement with the Moro National Liberation Front (MNLF), the country’s 

first Muslim revolutionary group. (The MILF broke away from the MNLF in 1977.) That 

agreement, which establishes autonomy in provinces and cities that voted to be part of 

the Autonomous Region in Muslim Mindanao (ARMM), ended the MNLF’s 25 years of armed 

struggle for independence. 

While the MNLF opted to achieve its aspiration for self-determination through autonomy, the MILF considers this vehicle for limited self-rule a total failure and renewed its 

demand for the establishment of an independent Muslim state. The MILF believes that 

autonomy has failed to address the fundamental grievances of the armed revolution and 

it declared ahead of the talks that it will reject the same or even an enhanced autonomy 

arrangement.2 On the other hand, Manila continues to reject any demand for a separate 

Muslim state in the southern Philippines. 

Notwithstanding the seemingly irreconcilable positions, the current talks should 

provide a much needed impetus to push the process forward. There are reasons to be 

optimistic. 

First, the government-MILF cease-fire is holding. Monitors from member countries 

of the Organization of the Islamic Conference (OIC)—specifically, Malaysia, Brunei, and 

Libya—are in the southern Philippines helping to implement the provisions of the ceasefire agreement. 

Second, the talks have a third-party facilitator. Since March 2001, Malaysia has been 

spearheading the peace initiatives in the southern Philippines on behalf of the Organization of the Islamic Conference. Playing a supporting role in facilitation is the United 

States Institute of Peace. 

ABOUT THE INSTITUTE

The United States Institute of Peace is an 

independent, nonpartisan federal institution 

created by Congress to promote the prevention, 

management, and peaceful resolution of international conflicts. Established in 1984, the Institute 

meets its congressional mandate through an array 

of programs, including research grants, fellowships, professional training, education programs 

from high school through graduate school, 

conferences and workshops, library services, and 

publications. The Institute’s Board of Directors is 

appointed by the President of the United States 

and confirmed by the Senate.

BOARD OF DIRECTORS

J. Robinson West (Chair), Chairman, PFC Energy, 

Washington, D.C. • María Otero María Otero (Vice Chair), President, (Vice Chair), President,

ACCION International, Boston, Mass. • Betty F. Bumpers, 

Founder and former President, Peace Links, Washington, 

D.C. • Holly J. Burkhalter, Advocacy Director, Physicians 

for Human Rights, Washington, D.C. • Chester A. Crocker,

James R. Schlesinger Professor of Strategic Studies, School 

of Foreign Service, Georgetown University • Laurie S. 

Fulton, Partner, Williams and Connolly, Washington, 

D.C. • Charles Horner, Senior Fellow, Hudson Institute, 

Washington, D.C. • Stephen D. Krasner, Graham H. Stuart 

Professor of International Relations, Stanford University • 

Seymour Martin Lipset, Hazel Professor of Public Policy, 

George Mason University • Mora L. McLean, President, 

Africa-America Institute, New York, N.Y. • Barbara W. 

Snelling, former State Senator and former Lieutenant 

Governor, Shelburne, Vt. 

MEMBERS EX OFFICIO

Arthur E. Dewey, Assistant Secretary of State for 

Population, Refugees, and Migration • Michael M. Dunn,

Lieutenant General, U.S. Air Force; President, National 

Defense University • Peter W. Rodman, Assistant 

Secretary of Defense for International Security Affairs 

• Richard H. Solomon, President, United States 

Institute of Peace (nonvoting)

2
Third, the organization of the talks has vastly improved since 1997. Now the parties 

have agreed to discuss their broad interests ahead of specific political structures. The June 

2001 Tripoli Peace Agreement between Manila and the MILF provided the framework and 

the guidelines for the conduct of the negotiations and includes a reference to the incremental characteristics of the peace process.3 This means that the current round of talks is 

to proceed in such a way that the three substantive issues—namely, “ancestral domain” 

(Muslims’ historical claim of the southern Philippines as their homeland), security arrangements in MILF areas, and rehabilitation of communities affected by conflict—will be 

tackled in stages, ahead of the discussions of mutually agreeable political structures. 

Fourth, civil society and international aid organizations are active participants in the 

peace process. Nongovernmental organizations (NGOs) such as the “Bantay Cease-Fire” 

(Cease-Fire Watch) are mobilizing to help implement the cease-fire agreement. Foreign 

governments and international aid organizations have pledged to provide funding for 

rehabilitation and postconflict development programs once a peace agreement with the 

MILF is in place. 

Origins of the Conflict 

Muslims in the Philippines make up 5 percent, or around 4 million, of the Philippines’ 

total population of 82 million. They are geographically concentrated in the islands of 

Mindanao and Sulu in the southern Philippines, where they constitute around 20 percent 

of the region’s population of more than 16 million. They belong to three major (and ten 

minor) ethno-linguistic groups: the Maguindanaoans in the Pulangi River Basin of central 

Mindanao, the Maranaos of the Lanao Lake region in central Mindanao, and the Tausugs 

in the Sulu archipelago. Muslims are in the majority in five provinces (Maguindanao, 

Lanao del Sur, Basilan, Sulu, and Tawi-Tawi) and in the Islamic City of Marawi, which are 

currently ARMM constituents. 

The Muslims’ historical claim on Mindanao and Sulu as their homeland predates the 

Spanish colonization of the Philippines that began with the arrival of General Legaspi in 

1565. As early as the latter part of the thirteenth century, local Islamic communities and 

settlements of foreign Muslims were already thriving in Sulu. The first sultan of Sulu came 

to power around 1450; Sharif Kabunsuan, who founded the Maguindanao sultanate, came 

to Mindanao around 1515. Thus, long before the Spaniards consolidated their control over 

the northern part of the Philippines, Islam was thriving in the southern islands, and the 

sultanates in Sulu and Maguindanao were already well organized. Trade and commerce by 

Muslim traders across the Malay regions and beyond were also flourishing. 

For three centuries, the Muslims in the south successfully resisted the incursions of 

the Spanish colonizers, who were able to establish a firm foothold only in the Christian 

North. As they called their enemies from Mauritania and Morocco, the Spaniards referred 

to the Muslims in the south as “Moros,” a term that later became a symbol of courage and 

nationhood for the Muslims in the Philippines. As the unconquered people of the South, 

the Moros were the masters of Mindanao and Sulu, where they constituted 98 percent of 

the population. 

But American colonization succeeded in subjugating the Muslim south by 1914. Aijaz 

Ahmad has identified the factors behind the relatively swift success of the Americans 

in contrast to the repeated failures of the Spaniards: First, the balance of forces: the 

Americans had sophisticated weapons and the ability to concentrate forces across the 

archipelago effectively. Second, a new model of colonial administration: the Americans 

allotted considerable administrative powers to governments at the municipal and district 

levels, which clinched their allegiance to the colonial authority. Third, the demographic 

model of colonization: entire populations, for the most part landless and ambitious, were 

encouraged to migrate from the Visayas and Luzon to create Christian enclaves in overwhelmingly Moro areas—that is, on lands the Muslims claimed as their own.4 At the time 

3

Since March 2001, Malaysia 

has been spearheading the 

peace initiatives in the southern Philippines on behalf of the 

Organization of the Islamic Conference. Playing a supporting 

role in facilitation is the United 

States Institute 

of Peace. 

The 9/11 terrorist attacks 

on the United States brought 

new prominence to the Islamic 

militancy in the Philippines, 

particularly in Mindanao, the 

country’s second largest island 

and the arena of the struggle 

for an independent Islamic state 

by the MILF.
the Philippine commonwealth was established in 1935, government policy was already 

geared toward assimilating the Moros into the larger Philippine society. 

As large Christian resettlement communities sprouted quickly in Mindanao from the 

1930s onward, the Moros became the minority in the land they considered their own; the 

proportion of Moro inhabitants to the total population fell from 98 percent to 40 percent 

by 1976, and to around 20 percent currently. Moros now own less than 17 percent of the 

property on the islands, mostly in impoverished areas in the countryside. By the latest 

estimates, 80 percent of the Moros are landless. 

From 1968 to 1971, political organizations composed mostly of Moro students waged 

numerous campaigns for the recognition of the Moros’ right to self-determination as a 

people with a distinct history and identity. These movements culminated in the establishment of the Moro National Liberation Front (MNLF), headed by Nur Misuari, a professor 

at the University of the Philippines. Hundreds of young Moros were sent to Malaysia for 

paramilitary training; Sabah in Malaysia became the supply and communication center of 

the Moro rebels. At the same time, violent incidents involving Christian and Moro paramilitary groups escalated. These incidents acquired a more ominous dimension in 1971, 

when the Philippine Constabulary sided with Christian paramilitary groups in offensives 

against the Moro rebels. 

On September 21, 1972, President Ferdinand Marcos declared martial law against the 

growing insurgency. The MNLF waged armed counteroffensives and demanded recognition for an independent state for the Bangsamoro (“the Moro homeland”). From 1972 to 

1976, military and civilian casualties reached 120,000. More than 100,000 people fled 

to nearby Malaysia, and around one million inhabitants of the southern Philippines were 

internally displaced. In 1975, the MNLF gained recognition from the Organization of the 

Islamic Conference as the representative of Muslims in the Philippines. President Marcos 

sued for peace and embarked on a flurry of diplomatic initiatives with OIC member states, 

which facilitated a cease-fire agreement and the opening of negotiations between the 

government and the MNLF. 

In December 1976, the Marcos government and the MNLF signed a peace pact in 

Tripoli that called for the establishment of autonomy in 13 provinces and 9 cities in the 

southern Philippines. But the two sides had serious disagreements on the implementation of the pact, particularly on the issue of a plebiscite. President Marcos unilaterally 

implemented the agreement and established provisionally autonomous governments in 

two regions that covered the provinces and cities under the Tripoli Agreement. The MNLF 

did not recognize the autonomous governments and accused the government of violating 

the terms of the Tripoli Agreement. It was not until the peace agreement in 1996, when 

former General Fidel Ramos was the Philippines’ president, that the MNLF and the Philippine government settled all questions on the implementation of the Tripoli Agreement 

and provided a formula for autonomy acceptable to the MNLF. 

4

MAJOR PHILIPPINE GOVERNMENT– MILF AGREEMENTS

• Agreement for General Cessation of 

Hostilities, July 18, 1997. 

Commits the Philippine armed forces and 

the MILF to a cease-fire.

• Tripoli Peace Agreement, July 22, 2001.

Sets the broad framework and guidelines on 

security and the conduct of the negotiations 

on the substantive aspects of the conflict.

• Implementing Guidelines of the Security 

Aspect of the Tripoli Peace Agreement, 

August 7, 2001.

Establishes local cease-fire monitoring teams 

and calls for the formation of monitoring 

teams from the Organization of the Islamic 

Conference. 

• Implementing Guidelines of the 

Humanitarian, Rehabilitation and 

Development Aspects of the Tripoli Peace 

Agreement, May 7, 2002.

Affirms the parties’ observance of 

international humanitarian law and provides 

guidelines for the rehabilitation and 

development of areas affected by conflict.

• Operational Guidelines of the Ad Hoc 

Joint Action Group, December 21, 2004.

Stipulates guidelines for isolating criminal 

activity within MILF areas.

As large Christian resettlement 

communities sprouted quickly 

in Mindanao from the 1930s 

onward, the Moros became the 

minority in the land they 

considered their own; the 

proportion of Moro inhabitants 

to the total population fell from 

98 percent to 40 percent 

by 1976, and to around 

20 percent currently. 

PROVINCES IN THE 

AUTONOMOUS REGION 

IN MUSLIM MINDANAO (ARMM)

IX Western Mindanao

 54. Basilan

 55. Sulu

 56. Tawi-Tawi

XII Central Mindanao

 70. Lanao del Sur

 71. Maguindanao

 54. Basilan

 55. Sulu

 56. Tawi-Tawi
Evolution of the Government–MILF Peace Process

In 1977, a group within the MNLF, led by vice-chair Salamat Hashim, tried to seize the 

movement’s leadership over differences in ideology and strategies. Salamat, a charismatic 

religious leader schooled at the Al-Azhar University in Cairo, later established the Moro 

Islamic Liberation Front in 1984. Under Salamat and a core group of ulamas (Islamic (Islamic

scholars), the MILF pursued a religious agenda, while MNLF chair Nur Misuari steered the 

MNLF in the direction of a nationalist and secular political movement. 

As the OIC’s sole recognized representative of Philippine Muslims, the MNLF was the 

recipient of government’s diplomatic and peace initiatives from 1977 until the signing of 

the 1996 peace agreement. While Manila negotiated with the MNLF, the MILF quietly built 

up its armed forces and mass base of supporters. By the time the Philippine government 

concluded negotiations with the MNLF, the MILF was already a formidable force, consisting of more than 12,000 armed fighters in 13 major camps and 33 satellite enclaves. 

With Islamic religious leaders holding top positions in the movement, the MILF wielded 

considerable influence over a large number of Muslim grassroots communities in central 

Mindanao. 

Right after signing the peace deal with the MNLF, President Ramos initiated similar 

talks with the MILF as part of the comprehensive Mindanao peace process. While the MILF 

rejected the Manila-MNLF accord, it responded favorably to Ramos’s overtures by participating in exploratory meetings to pave the way for formal negotiations. 

At the outset of the discussions, the MILF proposed a single talking point: a solution 

to the Bangsamoro problem, which, it held, involved a wide variety of social, cultural, 

economic, and political issues that included, but were not limited to, the following: 

recognizing Moros’ ancestral domain, their displacement and landlessness, reparations to 

war victims and for destruction of property, violations of their human rights, social and 

cultural discrimination against Muslims, policies that corrupt the mind and the moral 

fiber of the Moros, economic inequalities and widespread poverty among Muslims, exploitation by outsiders of the Moro homeland’s natural resources, and the need for genuine 

agrarian reform.

The MILF claimed that finding a lasting political solution to the problem should form 

part of the agenda in the formal talks, with the end in view of establishing a system of 

life and governance suitable and acceptable to the Bangsamoro people. Soliman Santos, 

who has documented the history of the MILF peace process, observes that the MILF’s reference to a “system” connotes a comprehensive approach to the Bangsamoro problem.5

The wording of this proposed MILF agenda is significant because, for the first time, the 

MILF officially acknowledged its openness to a political form that is not necessarily an 

independent state, but one that could possibly address Bangsamoro grievances. 

Santos notes that from 1996 to 2000, the government and the MILF entered into 

a total of 39 agreements, joint communiqués, acknowledgments, and resolutions: 16 

agreements on the implementation of the cease-fire pact (organization of committees, 

repositioning of government and MILF troops, return of evacuees, and safety and security 

guarantees), 13 on the framework of the talks, six on procedural matters, and four on 

recognition and verification of MILF camps. Throughout this period, no resolution was 

reached on the substantive issues raised by the MILF. 

In 2000, President Joseph Estrada launched major offensives against the MILF that 

Manila initially described as operations to free a major highway from MILF control. Later, 

it was apparent that the ultimate objective was for the government to regain control 

of MILF camps, some of which were acknowledged in earlier agreements, when military 

operations extended beyond the disputed highway and were terminated only after government troops established control over 47 major and satellite MILF camps. The all-out 

government offensives resulted in the suspension of the peace process, the shift in the 

MILF’s armed struggle from conventional to guerilla warfare, and the declaration by MILF 

5

On September 21, 1972, 

President Ferdinand Marcos 

declared martial law against 

the growing insurgency. The 

MNLF waged armed counteroffensives and demanded 

recognition for an independent 

state for the Bangsamoro 

(“the Moro homeland”). 

The wording of this proposed 

MILF agenda is significant 

because, for the first time, the 

MILF officially acknowledged 

its openness to a political form 

that is not necessarily an 

independent state, but one 

that could possibly address 

Bangsamoro grievances.
chairman Salamat of a jihad against the Philippine government. The MILF also scored the 

government for violating the cease-fire pact and agreements in which Manila acknowledged some MILF camps. 

Macapagal-Arroyo’s assumption of the presidency after Estrada was ousted in early 

2001 paved the way for the resumption of the MILF peace talks. She declared a unilateral 

cease-fire and initiated exploratory talks with the MILF. This time, Manila responded 

favorably to the three conditions proposed by the MILF: that the talks be mediated by 

the OIC or by an OIC member country, that the parties comply with the terms of past 

agreements, and that the talks be held in a foreign venue. Malaysia took an active role as 

third-party facilitator in the exploratory phases held in Kuala Lumpur. The first round of 

formal talks was held in Tripoli, where the parties agreed to the following: 

• The talks will revolve around the three main themes of security, rehabilitation, and 

ancestral domain.

• Both sides recognize that a Bangsamoro homeland is not necessarily incompatible 

with Philippine sovereignty and territorial integrity.

• Both sides acknowledge the existence of the Bangsamoro people and other indigenous peoples.

• The peace process will be conducted in stages and the grievances of the Moros will 

be addressed simultaneously with the peace process.

• There will be consultations with the Bangsamoro people and new formulas will be 

explored that will permanently respond to their aspirations.6

From November 2000 to February 2003, the negotiations resulted in the forging of the 

2001 Tripoli Peace Agreement; the Implementing Guidelines of the Security Aspect of the 

Tripoli Peace Agreement; the Manual of Instructions for the Coordinating Committee on 

the Cessation of Hostilities and the Local Monitoring Teams; the Joint Communiqué on 

Criminal Interdiction; and the Implementing Guidelines of the Humanitarian, Rehabilitation, and Development Aspects of the Tripoli Peace Agreement. 

In February 2003, the peace process was again suspended when government troops 

launched military offensives to take control of the MILF’s new headquarters in Buliok, 

Maguindanao. The withdrawal of the government troops from this key MILF enclave 

became one of the conditions of the MILF in agreeing to return to the negotiating 

table. The government, on the other hand, demanded that the MILF denounce terrorism 

and sever all ties with terrorist organizations. MILF chairman Salamat issued a public 

statement rejecting terrorism and denying his group’s ties to terrorist organizations. In 

July 2003, Salamat died of natural causes, and Al Haj Murad Ebrahim, the group’s vicechairman for military affairs, was named the MILF’s new leader. The government lifted 

arrest warrants issued against the MILF leaders for the series of bombings in the Philippines and repositioned its troops out of the MILF headquarters in Buliok. With these 

developments, the stage was set for the resumption of the formal talks on substantive 

issues in the secessionist conflict. 

This stage of the peace talks, to be held in Kuala Lumpur in February 2005, will tackle 

ancestral domain, the most complex and contentious issue, as evidenced by the wide 

disparity in definitions of the term by the MILF and the government. The MILF’s draft 

proposal on ancestral domain defines it as all lands and areas, including the environment 

and natural resources therein of the Bangsamoro people, established through occupation, 

possession, and dominion since time immemorial by cultural bond, customary law, historic 

rights, and legal titles. 

Although the government has consistently referred to the Indigenous People’s Rights 

Act as a framework for resolving the ancestral domain claims of the Bangsamoro, the MILF 

considers the law inadequate as it dilutes the Bangsamoro people’s sovereign rights to 

their homeland and considers the Moros as just one among many indigenous groups in the 

Philippines. For the MILF, the law is unresponsive to its demand for a system of life and 

governance that necessarily includes the Moro’s exercise of political and economic control 

6

The government, on the other 

hand, demanded that the MILF 

denounce terrorism and sever all 

ties with terrorist organizations. 

This stage of the peace talks, to 

be held in Kuala Lumpur in 

February, 2005, will tackle 

ancestral domain, the most 

complex and contentious issue, 

as evidenced by the wide disparity in definitions of the term by 

the MILF and the government. 
over their homeland. MILF vice-chair for political affairs Ghadzali Jaafar has said that “the 

root cause of the Moro revolution is Manila’s colonization, which paved the way for the 

country’s oligarchs to pillage the Bangsamoro people’s ancestral domain.”7 

To facilitate negotiations on ancestral domain, government and MILF panels formed 

working groups in December 2004 to try to arrive at common understandings of the four 

sub-issues of ancestral domain: concept, territory, governance, and resources. 

As to the issues of security and rehabilitation, the 2001 Tripoli Peace Agreement obliges the parties to observe the Agreement on the General Cessation of Hostilities signed 

on July 18, 1997. The Tripoli Agreement also empowered the MILF to lead and manage 

rehabilitation and development projects in conflict-affected areas. In that vein, the MILF 

established in 2002 the Bangsamoro Development Authority, which is spearheading the 

rehabilitation of areas affected by the conflict. The mechanisms for implementing the 

cease-fire have also been put in place with the strengthened Joint Coordinating Committees on Cessation of Hostilities and the establishment of the OIC International Monitoring 

Team, the Local Monitoring Teams, and the Ad Hoc Joint Action Group to stop criminal 

activity in the region. Civil society groups are also conducting their own “Bantay CeaseFire” (Cease-Fire Watch) operations that are significantly contributing to peacekeeping 

while the talks are going on. 

Although efforts to boost security and rehabilitation are under way, the parties 

will also be negotiating more permanent arrangements for the development of Morodominated areas and security for the Bangsamoro, which are tied up with the discussions 

on ancestral domain and political structures. The critical points in these discussions are 

disarmament and demobilization of MILF combatants and security arrangements for 

MILF-controlled areas.

Ripe for Resolution

Necessity and opportunity lend “ripeness” to the resolution of the conflict in Mindanao—

that is, the conflict has matured to the point where both sides see more advantages to 

ending it than to continuing the warfare. 

First, there is a growing realization in the Philippines that fighting it out on the 

battlefield simply does not work. The major wars of 2000 and 2003 did not bring Manila 

or the MILF any tactical advantage. In fact, the offensives were not only costly in terms of 

human casualties and civilian dislocations, but also led the MILF to wage guerilla warfare 

that proved more difficult for the government to contain. Yet taking over villages in the 

countryside, attacking military positions, and being ambiguous about its ties with terrorist groups obscured the legitimacy of the MILF’s cause and invited more military action 

from the government. The offensives also set back efforts to advance Christian-Muslim 

relations. Egged on by government propaganda, the country’s Christian majority overwhelmingly supported the offensives, threatening the transformation of the secessionist 

conflict into a religious war. 

Second, a negotiated settlement with the MILF is necessary to boost the country’s 

economy, which has been lagging behind those of its neighbors for years. The conflict 

in Mindanao is damaging the country’s image to outside investors as international media 

reports and foreign governments’ advisories restricting travel to the islands create the 

impression that the southern Philippines is a haven for terrorists and insurgents.8 The 

costly war with the MILF drains the nation’s coffers and boosts Mindanao’s image as a 

virtual war zone. 

Third, the government views a settlement with the MILF as a means to contain Islamic 

extremism in Southeast Asia. Certainly, the Muslim insurgency in Mindanao fuels Islamic 

militancy in the region, and a settlement with the MILF will be a big boost to the global 

War on Terror.

7

The critical points in these 

discussions are disarmament 

and demobilization of MILF 

combatants and security 

arrangements for MILFcontrolled areas.

Egged on by government 

propaganda, the country’s 

Christian majority overwhelmingly supported the offensives, 

threatening the transformation 

of the secessionist conflict into 

a religious war. 
Fourth, the emergence of new leaders in the MILF is believed to be an opportunity 

to reinvigorate the peace process and to seek fresh solutions. It is widely believed that 

the influence of moderate elements has been strengthened, raising expectations that the 

revolutionary group will demonstrate more flexibility in the negotiations. 

Fifth, the MILF’s openness to discussing its interests ahead of trying to clarify any 

political arrangement opens a wider range of options than the restrictive “independence 

or autonomy” proposition that hampered previous talks. The MILF is reportedly willing to 

pursue its agenda outside the 1976 Tripoli Agreement, which was the framework for the 

government’s discussions with the MNLF in 1996.9 By leaving that framework behind, it 

makes it more likely that the negotiated settlement will involve only areas where Muslims 

are in the majority—a proposition with a greater chance of succeeding. Also, by agreeing to discuss its grievances ahead of proposed political structures, the MILF is sending a 

strong signal that it does not intend to make the contentious issue of territory the centerpiece of the discussions, setting the stage for more interest-based and problem-solving 

negotiations, which dramatically heightens the prospects of a workable settlement. 

Sixth, the growing international attention the dispute has been getting in recent years 

raises the prospects for a peaceful settlement. Until 2001, the government considered 

the conflict a domestic issue, given OIC recognition of the MNLF as the sole and legitimate representative of Muslims in the Philippines. The MILF was likewise reluctant to 

seek international intervention after it rejected the OIC-brokered autonomy arrangement 

between the government and the MNLF. But the all-out war in 2000 unleashed by President Estrada apparently convinced the MILF of the need for some kind of international 

intervention to provide enforcement mechanisms for the provisions of agreements. Thus 

when Macapagal-Arroyo became head of state in 2001, the MILF agreed to resume talks 

only with OIC mediation. The assistance being provided by the OIC through Malaysia, the 

United States Institute of Peace, and the international community enhances the prospects for the conflict’s resolution. 

Challenges in the Talks

Despite the climate of optimism surrounding the talks between the government and the 

MILF, there is no guarantee that the talks will be successful. To be sure, there are some 

formidable obstacles along the path to a settlement. 

First, the government and the MILF must be able to formulate a workable and effective 

agreement that will bring sustainable peace and development to the southern Philippines. 

The growing concern is less with the parties reaching an agreement than with whether 

the agreement will address the fundamental causes of the conflict. The history of peace 

processes in the Philippines is replete with signed pacts that are good on paper but 

miserably short on implementation. The MILF definitely intends to leverage the perceived 

inability of the government to fulfill its commitments under its peace accord with the 

MNLF to demand stronger guarantees and enforcement mechanisms. 

Second, the parties will have to reconcile their divergent positions on the issue of 

political structures. Although the talks are designed to forestall discussions on the contentious issue of political structures, the parties will have to address it sooner rather than 

later. After all, negotiated settlements are essentially political deals, and issues such as 

ancestral domain, security, and rehabilitation cannot be resolved without a consensus on 

a certain kind of a political arrangement. Moreover, a political system must be put in place 

as a mechanism for effective implementation of any negotiated settlement. 

Some arrangements that will most likely figure in the discussions on political systems 

include any or a mix of the following: 

• A structure separate from the existing political system for the development of MILF 

communities; integration of MILF troops into the Armed Forces of the Philippines or 

8

Certainly, the Muslim insurgency 

in Mindanao fuels Islamic 

militancy in the region, and a 

settlement with the MILF will be 

a big boost to the global 

War on Terror.

Despite the climate of optimism 

surrounding the talks between 

the government and the MILF, 

there is no guarantee that the 

talks will be successful. 

To be sure, there are some 

formidable obstacles along the 

path to a settlement. 
the Philippine National Police; and the strengthening of institutions for “personal 

autonomy”, such as Islamic education and Sharia law. 

• Areas constituted as special zones, perhaps like Swiss cantons, where Muslims can 

exercise a higher degree of self-determination. 

• A new and expanded autonomous region with more powers. 

• A Muslim state under the federal system of government. 

• An independent state where Muslims are in the majority. 

MILF chairman Murad declares that the MILF would never compromise the right of the 

Bangsamoro people to self-determination and that his group will enter into a negotiated 

political solution that is just, lasting, and comprehensive.10 Ghadzali Jaafar, MILF vicechair for political affairs, says that the solution the MILF proposes is not autonomy, which 

he describes as a failure.11 Nevertheless, the government so far has not gone beyond the 

autonomy framework, proposing to the MILF a political package consisting of enhanced 

powers for the autonomous region and a possible expansion of its coverage. 

To reach common ground, it is imperative that the parties demonstrate openness in 

exploring all options for a political arrangement that can accommodate their conflicting 

interests. The “independence-autonomy track” that dominated past peace processes has 

proven to be too constricting. The features of other political arrangements, especially 

those resulting from negotiated settlements elsewhere, can be instructive. Institutions 

that specialize in managing international conflicts, such as the United States Institute 

of Peace, can provide invaluable inputs to the talks, particularly on effective models for 

postconflict governance. 

Both parties should demonstrate creativity, resiliency and openness in crafting political 

solutions that address the root causes of the conflict, a challenge that is more pronounced 

on the side of the government, whose options are limited by the Philippine constitution 

and statutes; the peace pact with the MNLF; and existing political structures, such as 

the local government units in Muslim areas and the ARMM. The constitution provides for 

the specifics of autonomy, including the powers that can or cannot be exercised by the 

autonomous region, thus foreclosing better arrangements out of negotiated settlements. 

In “constitutionalizing” autonomy, its distinct advantage as a flexible solution to the 

conflict is lost. The government and the MILF must view the negotiations as a problemsolving forum and be open to explore options that even go beyond existing political 

structures and the constitution in order to find effective solutions to the nagging issues 

of peace and development in the southern Philippines. 

However, the two sides must also be able to build on structures that may have failed 

but that have nevertheless inched empowerment forward for the Muslims. A survey of 

the legal instruments for autonomy in the southern Philippines shows a distinct pattern of power transfers to the region since the grant of autonomy in 1977. It would be 

counterproductive to totally ignore the strides that have already been achieved in giving 

more self-determination to the Muslim minority. The task of nation building is always 

incremental and slow, but by taking this route, the government and the MILF can possibly 

institute profound changes while at the same time weaving existing political structures 

into a coherent and effective vehicle for genuine Muslim self-determination. 

Third, the parties will have to build strong and broad support for the peace process, 

most likely requiring compromises that may not sit well with their respective constituencies. As in any peace process, the talks will be shepherded by moderates from both sides 

who have to contend with extremists unwilling to enter into any form of compromise. 

Already, a group within the MILF has threatened to repudiate any agreement that does 

not grant independence to Muslims. On the part of the government, there are officials who 

believe that a more “hawkish” approach, not diplomacy, is the key to resolve the conflict. 

Many believe that the hard-liners can be won over if President Macapagal-Arroyo takes a 

9

The government and the MILF 

must view the negotiations as 

a prolem-solving forum and be 

open to explore options that 

even go beyond existing political 

structures and the constitution 

in order to find effective solutions to the nagging issues of 

peace and development in the 

southern Philippines. 

The “independence-autonomy 

track” that dominated past 

peace processes has proven to 

be too constricting. The features 

of other political arrangements, 

especially those resulting from 

negotiated settlements elsewhere, can be instructive.
10

personal approach and demonstrates strong political will to make the process a genuine 

forum to resolve the root causes of the conflict. 

Other potential “spoilers” who will need to be assuaged include members of the Philippine elite, whose hold on political and economic power is threatened by any settlement. 

Among them are local political leaders and groups that have substantial economic interests in continuing the armed conflict, including some elements in both the military and 

the MILF who benefit legitimately or otherwise from large budgets in times of war. 

While not totally against a settlement, many political leaders of Christian-dominated 

areas will accept a peace agreement only if it satisfies two requirements: first, that it 

will involve only the Muslims and the existing autonomous region (recently, a mayor in 

Mindanao refused to allow the formation of an international monitors office in his city, 

saying that his area is not within the area of conflict) and, second, that the agreement 

does not exact even an inch of concession from the Christian majority. 

This “bystander mentality” does not bode well for achieving a workable settlement. As 

part of the Bangsamoro problem, the Christian majority must be a part of the solution. 

One of the causes for the failure of implementation of the 1996 peace agreement with the 

MNLF is the lack of support from most Christian national and local government leaders. 

The Philippines’ Christian-dominated legislature, threatened by the growing influence of 

the Muslims, crafted the enabling law of the pact in a way that diluted or changed the letter and spirit of the accord. For instance, the law that was passed considerably weakened 

the broad fiscal autonomy granted to the autonomous region under the peace agreement. 

Also, the structures for peace and development, such as the Southern Philippines Council 

for Peace and Development and its Consultative Assembly, received little or no support 

from government officials. 

For the talks to succeed, support for the process, especially among the Christian majority, must be harnessed. The Christian majority cannot have it both ways: continuing to 

act as bystanders in the peace process averse to make any concessions while hoping for 

peace in Mindanao and progress for the country. If the Christian majority wants Mindanao 

to remain part of the Philippines and if it believes that peace in this part of the country 

is important to the nation’s progress, it must actively support the peace process and 

demonstrate its readiness to make sacrifices. 

The Organization of the Islamic Conference continues to recognize the MNLF, not the 

MILF, as the representative of the Muslims in the Philippines, so the MILF’s lack of legitimacy to speak for the Bangsamoro people in this regard is also a potential spoiler that 

can scuttle the talks or at least limit the coverage of any settlement to MILF communities 

and combatants. And there are divisions within the Bangsamoro along ethno-linguistic 

lines, as well as political fissures as a result of the conflict and the government’s integration policy. Moro leadership is exercised in conflict with or exclusively by and among 

traditional leaders, political families, religious leaders, the MNLF, and the MILF. There are 

persistent reports of cracks within the MILF along crucial issues of leadership, religious 

and political ideology, and positions in the peace talks. To settle the representation issue, 

the MILF has been consistent in its position for holding a referendum to determine once 

and for all the true will of the Moros with regard to their political future. 

With or without a referendum, it is clear that unless a peace pact has the broad support of the Moros, any comprehensive solution is bound to fail. Thus, the MILF must be 

able to build coalitions with other Moro leaders and civil society groups to support the 

peace process. It must galvanize the support especially of Islamic religious leaders who 

wield strong influence over the country’s Muslim population. It must solidify its 2001 

unity agreement with the MNLF in the context of the peace process, where the common 

interests of the two revolutionary groups can be brought into the talks.12 On the other 

hand, the government should exercise its influence and authority over mainstream Moro 

political leaders to support the peace process. 

Fourth, the government, the MILF, and international monitors must keep the fragile 

cease-fire in place to maintain an environment conducive to fruitful talks. Since 1997, 

Many believe that the 

hardliners can be won over if 

President Macapagal-Arroyo 

takes a personal approach and 

demonstrates strong political 

will to make the process a 

genuine forum to resolve the 

root causes of the conflict. 

With or without a referendum, 

it is clear that unless a peace 

pact has the broad support of 

the Moros, any comprehensive 

solution is bound to fail.
11

the peace process has been constantly derailed because of charges and countercharges 

of cease-fire violations. Although the cease-fire mechanism at this stage of the talks is 

potentially more effective, the government’s intensified drive ostensibly against terrorists in MILF-controlled areas remains a potential disruption. On November 19, 2004, the 

Philippine military launched an air assault against an MILF-controlled area that the 

government claimed was the site of a meeting of suspected members of Abu Sayyaf and 

Jemaah Islamiyah. The MILF has denied that such meeting was taking place and has since 

filed a protest before the International Monitoring Team. Regardless of their veracity, 

the alleged links of the MILF to terrorist networks can be used as a convenient justification for military operations, which can lead to the collapse of the peace process. On the 

other hand, the persistent reports that the MILF is coddling suspected terrorists must be 

addressed in a timely and credible fashion. 

The head of the international monitors has been quoted as saying that it is not within 

their mandate to investigate alleged MILF-terrorists links.13 But without making a determination on such charges, it is doubtful whether they can definitely say the cease-fire 

has been violated in cases similar to the November 19 assault. Thus, it is imperative that 

third-party facilitators and monitors act more decisively on the issue of the MILF’s ties to 

terrorists to avert “spoilers” from exploiting this vulnerable spot in the process. 

Fifth, the parties will have to fast-track the talks while ensuring that the agreement 

is comprehensive, workable, and responsive to Moro grievances. Certainly, there are no 

instant solutions to complex conflicts like the one in Mindanao. It is important, however, 

that parties’ respective constituencies see that the talks are making significant progress. 

Moreover, if the talks appear to be wandering, they will be more susceptible to “spoilers” 

sabotaging the process. As a compromise, the parties may concur on a multiphase agreement whose more vital components can be readily implemented even while the process is 

continuing. In this way, the talks can produce concrete results in the intermediate term 

that can galvanize support for agreements on the more contentious issues. 

Sixth, the government and the MILF must be able to clearly identify available sources 

of funding to implement any agreement effectively. The rehabilitation of conflict-affected 

areas, as well as the creation of salutary political and economic infrastructures, will entail 

huge costs. Yet the Philippines faces a fiscal crisis brought about by a ballooning budget 

deficit and soaring public debt. Although the international community has rehabilitation 

funds at the ready once a peace pact is signed, its resources are not limitless, and the 

money, in most cases, is tied to specific programs. The two sides must learn from the 

implementation failures of the MNLF peace pact, caused mainly by funding shortages and 

accountability issues. The government and the MILF must therefore come to terms with 

the fiscal aspects of any negotiated settlement, coordinate with the donor community to 

optimize the use of donor money, and set up adequate safeguards to ensure the judicious 

use of funds. 

Conclusion 

While the MILF peace process is one important piece in building lasting peace and 

development in the southern Philippines, it is by no means an instant solution to all 

the problems of instability and underdevelopment in the region. The long history of and 

failed approaches to the conflict have so deeply divided the inhabitants of the southern 

Philippines that any roadmap is likely to be met with skepticism or, at the most, guarded 

optimism. Whether the MILF peace process will be any different depends on the willingness and the capacity of the parties to go beyond their group interests. 

It is clear that in the present talks, no effort was spared to ensure that the parties 

could reach an agreement; there seems to be no question about the resolve of the government and the MILF. The greatest concern of many is no longer about the parties signing 

a peace pact but whether the Filipino nation can embrace it as its common roadmap for 

Regardless of their veracity, 

the alleged links of the MILF to 

terrorist networks can be used 

as a convenient justification for 

military operations, which can 

lead to the collapse of the 

peace process.

The two sides must learn from 

the implementation failures of 

the MNLF peace pact, caused 

mainly by funding shortages 

and accountability issues.
peace and prosperity in Mindanao. It is only when there is real national consensus on 

this roadmap that the terms of the peace pact can be implemented in a way that directly 

addresses the grievances of the Moro people. Thus, the following components of the peace 

process must be strengthened: 

• Both sides must build a national consensus on the roadmap agreed upon during 

the negotiations by conducting more consultations on the issues discussed in the 

negotiations. The government must reach out to the leaders of the Christian majority, 

particularly members of Congress and local officials. The MILF must reach out to the 

MNLF, as well as to Muslim traditional leaders. 

• Christian and Muslim religious leaders must take the lead in rallying their own people 

to support the peace process. The Bishop-Ulama Forum, a conference of Christian and 

Muslim religious leaders in the Philippines, must be actively involved in harnessing 

this support. 

• The government and the MILF must provide strong and effective mechanisms for the 

implementation of the peace pact. A neutral third party must be named to directly 

oversee faithful compliance of Manila and the MILF with the terms of the agreement. 

• Funding for implementation must be clearly identified and allocated in a way that 

insulates it from partisan and personal interests of any group or party. 

NOTES

1. In her book, Seeds of Terror: An Eyewitness Account of al Qaeda’s Newest Center of Operations in 

Southeast Asia (New York: The Free Press, 2003), CNN correspondent Maria Ressa cites numerous classified police and military intelligence reports of the MILF’s links with al Qaeda and Jemaah Islamiya. 

Similar claims are made in the International Crisis Group’s report, Southern Philippines Backgrounder: 

Terrorism and the Peace Process. Asia Report, no. 80 (Singapore/Brussels: International Crisis Group, 

July 13, 2004).

2. “Autonomy not answer, say Moro rebs,” Philippine Daily Inquirer Philippine Daily Inquirer (Manila), October 13, 2004, (Manila), October 13, 2004, 

quoting MILF vice-chair for political affairs Ghadzali Jaafar. Online. Available: http://news.inq7.net/

regions/index.php?index=1&story_id=14799. 

3. This interim pact is referred to as the Government of the Republic of the Philippines-MILF Tripoli 

Agreement on Peace of 2001, which should not be confused with the Tripoli Agreement between the 

government and the Moro National Liberation Front signed on December 23, 1976.

4. Ahmad Aijaz, “Class and Colony in Mindanao,” in Rebels, Warlords and Ulama: A Reader on Muslim 

Separatism and the War in Southern Philippines, ed. Eric Gutierrez et al. (Quezon City: Institute for 

Popular Democracy, 1999), 5–6.

5. Soliman Santos, “Dynamics and Directions of the Peace Negotiations Between the Philippine 

Government and the Moro Islamic Liberation Front” (Quezon City, 2004), 6.

6. 2001 Philippine Government–MILF Tripoli Agreement.

7. Romy Elusfa, “MILF enthusiastic to tackle ‘ticklish’ ancestral domain issue,” Mindanews, November 

4, 2004, quoting MILF vice-chair Jaafar. Online. Available: http://www.mindanews.com/2004/11/04nwsmilf.html.

8. The governments of Canada, Japan, Australia, New Zealand, the United Kingdom, and the United 

States periodically issue advisories that restrict travel of their citizens to Mindanao and Sulu because 

of security concerns. The American Chamber of Commerce of the Philippines has recommended that the 

Philippines needs to educate the outside world that the security situation is not as bad as portrayed by 

international news reports and travel advisories; see The Roadmap to More Foreign Investment (Manila: 

American Chamber of Commerce of the Philippines, Inc., March 2003).

9. Elusfa, “MILF enthusiastic.”

10. “Autonomy not answer.”

11. Ibid.

12. The 2001 MNLF-MILF unity agreement in Kuala Lumpur created the Bangsamoro Solidarity Council 

to explore areas of cooperation between the two revolutionary groups in advancing the peace process. 

13. “Gov’t rules out terror links between MILF, JI,” Philippine Daily Inquirer Philippine Daily Inquirer (Manila), October 21, (Manila), October 21, 

2004, quoting Malaysian Major General Zulkifeli bin Mohd Zin, head of the international cease-fire 

monitoring team. Online Available: http://news.inq7.net/breaking/index.php?index=2&story_id=15621.

It is only when there is real 

national consensus on this roadmap that the terms of the peace 

pact can be implemented in a 

way that directly addresses the 

grievances of the Moro people.

An online edition of this report can be 

found at our website (www.usip.org), 

together with additional information 

on the subject.

United States 

Institute of Peace

1200 17th Street NW

Washington, DC 20036

www.usip.org