Jabarkan Command arrangements dari Forcas Defensa Timor Lorosa'e dalam bahasa tetun

A Constituição de estados de Timor Orientais que o Presidente é o xefe supremo da força de defesa e tem o poder para designar o xefe do F-FDTL e Chefe de Pessoal. O Council Oriental de Ministros e National Oriental é responsável para fundar o F-FDTL e fixar política relativo à segurança de Timor Oriental. Prime Minster Gusmão also serves as the current Minister of Defence and Security. A Superior Council for Defence and Security was also established in 2005 to advise the President on defence and security policy and legislation and the appointment and dismissal of senior military personnel. The council is chaired by the President and includes the Prime Minister, the defence, justice, interior and foreign affairs ministers, the heads of the F-FDTL and PNTL a national state security officer and three representatives from the national parliament. The council's role is not clear, however, and neither it nor the parliament served as a check against the decision to sack large numbers of F-FDTL personnel in 2006. A parliamentary committee also provides oversight of East Timor's security sector.

A small Ministry of Defence (which was renamed the Ministry of Defence and Security in 2007) was established in 2002 to provide civilian oversight of the F-FDTL. A lack of suitable staff for the Ministry and the close political relationship between senior F-FDTL officers and government figures rendered this oversight largely ineffectual and retarded the development of East Timor's defence policy up to at least 2004. The failure to institute effective civilian oversight of the F-FDTL also limited the extent to which foreign countries are willing to provide assistance to the F-FDTL and contributed to the 2006 crisis. As at early 2010 the Ministry of Defence and Security was organised into elements responsible for defence (including the F-FDTL) and  security (including the PNTL), each headed by their own Secretary of State. At this time the East Timorese Government was working to expand the Ministry's capacity with assistance from UNMIT, but continuing shortages of qualified staff limited the extent to which the Ministry could provide civilian oversight to the security sector.