Former ambassador to Israel, journalist and Jakarta-based diplomat Peter Rodgers. Credit:Lyn Mills LMZ It also says "the enemy are daily torturing, raping and executing the captured population" at a detention camp near Bacau. This phase in the release is underlined by a diplomat, with the comment added "sounds like fun". Another handwritten comment observes: "sound like the population must be in raptures." Another handwritten annotation by a diplomat jokes: "This [Fretilin] report is internally inconsistent. If 'the enemy was impotent', as stated, how come they are daily raping the captured population? Or is the former a result of the latter?" 'Sounds like fun' is written in the margin by Australian embassy officials.

The memo and its annotations were found in the National Archives by two researchers from Monash University, Sara Niner and Kim McGrath. The memo, said Dr Niner, was "vivid evidence of the lack of empathy and concern for human rights abuses in East Timor" in the Department of Foreign Affairs (DFA). "The archives in Canberra reveal that this culture of cover up is closely tied to DFA's need to recognise Indonesian sovereignty over East Timor so as to commence negotiations over the petroleum in the Timor Sea." The boundary negotiated in the early 1970s with Indonesia was highly favourable to Australia but left a gap in the border – the so-called Timor Gap as East Timor was then a Portuguese colony. Before Indonesia's invasion in 1975, Australia's ambassador in Indonesia Richard Woolcott​ cabled Canberra to observe the gap in the sea border "could be much more readily negotiated with Indonesia".

Australia has declined to negotiate a permanent boundary since East Timor's independence, with the fledgling state waiting to hear if Prime Minister Malcolm Turnbull will begin talks. Fairfax Media contacted members of the Jakarta embassy staff at the time who received the document. Cavan Hogue – who later rose to become an ambassador in the Soviet Union and Thailand – said he had just arrived at the embassy but could have penned at least one of the annotations, notably the joke about Fretilin being "internally inconsistent". "It does look like my handwriting," he said. "If I made a comment like that, being the cynical bugger that I am, it would certainly have been in the spirit or irony and sarcasm. It's about the press release, not the Timorese. That's how I'd interpret it."

Peter Rodgers, who is named on the memo as a recipient, declined to clarify if he authored any annotations but did offer his views in two brief emails.. "Those in the embassy in 1976 had no more reason to believe Fretilin propaganda than they did to believe Indonesian, UDT [Fretilin's local conservative rivals], Apodeti [a party favouring Indonesian integration] propaganda over the situation in East Timor," he said. "The commentary was blunt but this was on claims made by one of the protagonists in a messy, propaganda-rich, conflict." However, the Fretilin "propaganda" was broadly accurate. The United Nations-sponsored 2500 page report into violence in East Timor during the occupation found thousands of instances of sexual violence, forced starvation, summary executions and torture. "Rape, sexual slavery and sexual violence were tools used as part of the campaign designed to inflict a deep experience of terror, powerlessness and hopelessness upon pro-independence supporters," the report said.

"It was common practice for members of the Indonesian security forces to keep East Timorese women in detention in military bases. "These women, who were sometimes detained for many months and sometimes years, were often raped on a daily basis or on demand by the officer who controlled them, and often also by other soldiers." As many as 180,000 people died between 1975 and 1999, about one-third of East TImor's pre-invasion population.The peak for death, torture and starvation was between 1975 and 1979. In 1979, Mr Rodgers – who left the embassy to become a Fairfax correspondent in Jakarta – defied Indonesia's military to publish photos of starving Timorese in the Sydney Morning Herald and The Age. Mr Rodgers received the Australian journalist of the year award. But, while the photos galvanised outrage around the world, Mr Rodgers' reportage later received criticism for downplaying Indonesia's role.

"Deprivation was well established as a way of life long before the war," Mr Rodgers wrote in a series of articles. "The upheaval in the territory of the past four years should not be confused with deliberate intent on Indonesia's part." Loading Mr Rodgers, returned to the diplomatic corps and rose to become ambassador to Israel from 1994-1997. He is now an author on Middle East affairs and academic at the Australian National University. Mr Hogue, who has retired, said on Sunday there were "atrocities on all sides" and that people of goodwill believed it would be better for East Timor's people if they were part of Indonesia and not a "banana republic dependant on foreign aid".