Recently declassified US intelligence documents reveal Washington's passivity in the face of violence doled out by the Indonesian armed forces and the anti-separatist militias they formed in the run-up to the East Timor independence referendum two decades ago.
The more than 200 documents, which Efe has accessed, detail the US foreign policy in the region ahead of the referendum on 20 August 1999 that put an end to 24 years of Indonesia's bloody military occupation of the former Portuguese colony.
More than 1,500 Timorese were killed and over 250,000 were displaced as the island plunged into violence in the months before the vote.
The documents, which include diplomatic telegrams, intelligence reports and government memos, were released following a petition from the National Security Archive, a research non-profit at the George Washington University in Washington D.C.
Bradley Simpson, an academic who leads the team that published the documents, believes that the then-US president, Bill Clinton, should have halted arms deals with Indonesia sooner and pressed for an intervention of United Nations peacekeepers in East Timor.
He said: "It is important to note US knowledge of the overwhelming evidence of Indonesian military involvement in the arming, directing and working with militias in East Timor as they were both terrorizing the place from Jan-August 1999, and the general US refusal to do anything about these until East Timor was destroyed in early September."
The oldest document, a State Department Bureau of Intelligence and Research report on East Timor dated 28 January 1999, analyzed the decision of Indonesia's erstwhile president, Bacharuddin Jusuf Habibie, to permit the referendum in the first place.
The report flagged "the military's decision to arm pro-integration (pro-Jakarta) civil militias."
As soon as the independence referendum was announced, these pro-integration paramilitaries launched a campaign of violence and intimidation against pro-separatists.
The head of the Indonesian army at the time, General Wiranto, denied any involvement with the paramilitaries.
Another report from the State Department dated 26 February 1999 said the Indonesian military was "arming small, roving bands of East Timorese paramilitary groups to create unrest and portray the security situation as 'incipient civil war'."
Then, in April 1999, pro-Indonesia militias carried out a massacre in the coastal town of Liquica, killing around 50 civilians taking shelter in a church.
A memo from Phyllis Oakley, the assistant secretary for intelligence and research, to the then-secretary of state, Madeleine Albright, said: "prospects are high that a cycle of intimidation and terror will intensify."
Two weeks later, the UN Mission of Support in East Timor put 12,000 troops on the ground, but the armed groups turned their gaze towards journalists and international observers.
Embassies braced to evacuate foreign nationals.
On polling day, 98 of the electorate turned out to vote, a clear 78.5 percent them chose independence.
Hours after the results were made public, Indonesian troops and militias embarked on a fresh wave of violent reprisals, committing assassinations, burning buildings and razing whole towns.
Finally, on 9 September, the Clinton Administration suspended US military relations with Indonesia amid international pressures.
The measures also forced Indonesia to accept the arrival of a new Australian-led peacekeeping mission and to withdraw its troops from the fledgling nation of East Timor.
While East Timor was burning, days before Clinton cut off military relations with Indonesia, the then US ambassador to Jakarta, J. Stapleton Roy, met with an Indonesian military general.
"(The US) does not want East Timor to further damage ties between the two nations," he said.
The general told Roy that he "should not forget the starting point" in East Timor, whereby Indonesia received both US and Australian support for its invasion and subsequent occupation of the territory.
Overall, around 200,000 people were killed under Indonesian rule in East Timor, often assassinated or through illness. EFE-EPA