Andrew West – Australian Government officials have been accused of burying a crucial intelligence report about a 1998 Indonesian massacre in the West Papua town of Biak because it did not want to offend Indonesia so soon after it had thrown off the Soeharto dictatorship.

In a stunning and unorthodox attack on foreign policy by a serving member of the Australian Defence Force, intelligence officer Andrew Plunkett says the suppression of the Biak report all but encouraged Indonesia to arm and train pro-Jakarta militias in East Timor.

"We were saying Indonesia's behaviour in Biak was acceptable by turning a blind eye and not raising an official public protest," said Captain Plunkett, who served with Interfet in East Timor. "We were giving a green light to their subsequent actions," he said. "Biak was a dress rehearsal for the TNI [Indonesian army] in East Timor."

Fourteen months later East Timor was aflame as militias attacked, murdered and dismembered hundreds of civilians while the TNI looked on.

Canberra's response to the Biak massacre of July 6, 1998 – in which more than 20 people were killed and up to 200 were beaten, tortured or raped – was muted. A Department of Foreign Affairs and Trade (DFAT) spokeswoman said Foreign Minister Alexander Downer had raised media reports of the massacre with his Indonesian counterpart, Ali Alatas.

But Mr Downer did not know the extent of the slaughter because the official intelligence report had not been compiled by Major Dan Weadon, an intelligence officer attached to the Jakarta embassy. It took five months before DFAT publicly expressed "grave concerns" at the massacre.

Captain Plunkett made his comments after The Sun-Herald this week received copies of confidential e-mails he exchanged with Major Weadon. Major Weadon, who did not authorise the release of the e-mails, was sent to Biak from July 11 to 14 to investigate the slaughter, gathering eyewitness accounts and interviewing Colonel F.X. Agus Edyono, the chief of the local military command.

DFAT classified his report "confidential" instead of the usual "restricted", so it would not embarrass Indonesia. When Greens Senator Bob Brown asked the Government to release it, Senator Jocelyn Newman, representing then Defence Minister John Moore, refused, saying the report was "a highly classified document".

"Although some of the information given in the report is already in the public domain," she said, "the report provides far greater detail and amalgamates a number of sources of information. I believe, therefore, it provides a mass of information that in its totality would be very damaging to our international relations." But Major Weadon said: "In all probability [it] was capable of being downgraded, probably to unclassified."

In the e-mails, dated February 3, Major Weadon wrote to Captain Plunkett: "During my visit to [Edyono] I had expressed (as an official representative of Australia) disapproval of their actions, so to a degree Australia had condemned the actions (not sure, but Downer probably said something at a much higher level)... "Government/DFAT types probably took the stance that our point had been made, and why ruin all chance at further access/dialogue to score a few more points. The view is/was that we cannot bully the Indonesians into becoming a better nation – if so, they will simply tune out to us."

Major Weadon described Edyono as "polite and friendly, but obviously very suspicious and wary that my visit was going to discredit ABRI [Indonesia's armed forces]/Indonesia". "Anyway," he wrote, "I think I summed up the info by saying it was almost certain ABRI had responded in a very heavy-handed manner on 6 July 98, and ... were likely to have beaten, killed and tortured many people.

"From my point of view, the whole Javanese/Indonesian culture is to blame – they honestly believe they did the right thing and cannot understand why we criticise them for putting down traitorous primitive and racially inferior subversives."