As what have been designated "new missions", the F-FDTL has been given responsibility for crisis management, supporting the suppression of civil disorder, responding to humanitarian crises and facilitating co-operation between different parts of the government.

The widespread violence and destruction that followed the independence referendum in 1999 and the need to provide employment to FALINTIL veterans led to a change in policy.

[5] The inadequate number of police officers who were deployed to East Timor as part of the United Nations-led peacekeeping force contributed to high rates of crime.

Critics of the F-FDTL's establishment argue that as East Timor does not face any external threats the government's limited resources would be better spent on strengthening the PNTL.

While East Timor's political leadership recognised that the country does not currently face an external threat, they believed that it is necessary to maintain a military capacity to deter future aggression.

[21] Furthermore, UNTAET failed to establish adequate foundations for the East Timorese security sector by developing legislative and planning documents, administrative support arrangements and mechanisms for the democratic control of the military.

[23] The F-FDTL conducted its first operation in January 2003 when an army unit was called in to quell criminal activity caused by west Timorese militia gangs in the Ermera district.

[25] These problems have been driven by uncertainty over the F-FDTL's role, poor conditions of service due to limited resources, tensions arising from FALINTIL's transition from a guerrilla organisation to a regular military and political and regional rivalries.

On 24 April, the petitioners and some of their supporters held a four-day demonstration outside the Government Palace in Dili calling for the establishment of an independent commission to address their grievances.

On 3 May Major Alfredo Reinado, the commander of the F-FDTL's military police unit, and most of his soldiers including Lt Gastão Salsinha abandoned their posts in protest at what they saw as the army's deliberate shooting of civilians.

A United Nations inquiry found that the interior and defence ministers and the commander of the F-FDTL had illegally transferred weapons to civilians during the crisis and recommended that they be prosecuted.

The King's College study team strongly recommended against such a force structure, labelling it "unaffordable" and raising concerns over the impact of conscription upon East Timorese society and military readiness.

The team estimated that sustaining such a force structure would cost 2.6 to 3.3 per cent of Timor-Leste's annual gross domestic product and would "represent a heavy burden on the East Timor economy".

On 11 February 2008, a group of rebels led by Alfredo Reinado attempted to kill or kidnap President Ramos-Horta and Prime Minister Gusmão.

A joint F-FDTL and PNTL command was established to pursue the surviving rebels and the military and police demonstrated a high degree of co-operation during this operation.

While the joint command contributed to the surrender of many of Reinado's associates, it has been alleged that members of this unit committed human rights violations.

[50] However, the East Timorese government placed a high priority on re-establishing the F-FDTL and developing it into a force capable of defending the country.

The Strategic Defence and Security Concept also called for the F-FDTL's naval capabilities to be improved to adequately protect Timor-Leste's exclusive economic zone.

[1] Similarly, a 2019 Stockholm International Peace Research Institute noted that there has been little progress in completing the acquisition program set out in the Force 2020 plan, likely due to a shortage of funds and "possibly also because there seems to be no rationale for acquiring some of the equipment".

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 Timor-Leste's defence policy up to at least 2004.

[74] Although the army is small, the guerrilla tacticsemployed by FALINTIL before the departure in 1999 of the Indonesian National Armed Forces were effective against overwhelming numbers and it has the potential to form a credible deterrent against invasion.

[82] An assessment of Timor-Leste's security forces published by the Centre for International Governance Innovation in 2010 stated that "F-FDTL weapons management and control systems, while superior to that of PNTL, are underdeveloped".

[18] The role of the naval component is to conduct fishery and border protection patrols and ensure that the maritime line of communication to the Oecussi enclave remains open.

[90][91] This acquisition was controversial in Timor-Leste due to a perceived lack of transparency regarding the purchase and concerns that the patrol boats were not suited to the rough sea conditions and tropical weather in which they would need to operate.

[94] The East Timorese government also ordered two fast patrol boats from the Indonesian company PT Pal in March 2011 for the price of $US40 million.

[1] In 2019 the East Timorese Government was considering purchasing three Chinese variants of the Mil Mi-17 helicopter, and a small number of F-FDTL personnel were trained to operate the type in the Philippines.

The US military has stated that the purpose of this agreement is to support the creation of an Air Component to "help the Timorese government improve its maritime awareness, respond to natural disasters, and promote economic development".

These units formed an important part of the King's College report's option 3 force structure and their absence may have impacted on Timor-Leste's defence policy.

Timor-Leste is one of Brazil's main destinations for aid and the Brazilian Army is responsible for training the F-FDTL's military police unit (Maubere Mission).

While movements of people and drug smuggling across their international border has caused tensions, both countries have worked with the UN to improve the security situation in the region.