Hamish McDonald – The Australian Government sat on explosive intelligence material which showed the direct involvement of senior Indonesian army generals in the violence which swept East Timor in 1999.

Defence sources in Canberra have given details of how Australian electronic eavesdroppers intercepted secret messages between the Indonesian officers who ran a campaign of fear to deter the East Timorese from voting for independence.

But virtually none of the collected evidence, which could be vital to finding the masterminds responsible for crimes against humanity, has been shared with United Nations investigators. This is because of concerns that Indonesia would adopt countermeasures to foil future interception operations by the Defence Signals Directorate.

Transcripts of the DSD intercepts revealed to the Herald show a covert chain of command down from the then President B.J. Habibie's co-ordinating minister for politics and security, General Feisal Tanjung, to army generals and colonels on the ground in East Timor. It provides evidence for the first time that Tanjung, a career special forces and paratroop officer, used a network of similar minded officers in a campaign to avert a vote for independence in the United Nations-supervised ballot on August 30, 1999.

When this failed to their enormous surprise, a DSD intercept shows the officers then organised the forced deportation of one third of East Timor's population and the destruction of infrastructure, with the assistance of two other ministers in Habibie's cabinet the former generals A.M. Hendropriyono and Mohammad Yunus Yosfiah.

Three Indonesian army and police generals who were in charge of security for East Timor in 1999 are among 18 suspects whose trials begin in Jakarta today over four militia rampages in Liquica, Dili and Suai. But the generals who planned and directed the militia operation appear likely to escape indictment.

The leak of highly classified intelligence material is the first time raw DSD intercepts relating to a contemporary event have been disclosed. It reflects deep disquiet in defence circles that Canberra at first downplayed the high-level Indonesian military involvement with the militias blaming it on "rogue elements" and since then has not used it to help war crimes investigations.

Intercepts in February 1999 show Jakarta had sent detachments of special forces, code-named Tribuana and Venus, to begin black operations in East Timor, and that a commander based in Bali, Major-General Mahidin Simbolon, was referring to a militia group as "his crew".

As the militia campaign geared up with massacres of independence supporters in April, the DSD picked up conversations in which the East Timor army commander, Colonel Tono Suratman, is supervising the notorious militia leader Eurico Guterres.

Other messages include the allocation of radio frequencies by the Indonesian military command in Jakarta to militia groups, and a general in Jakarta's military intelligence agency organising T-shirts for demonstrations against the United Nations mission supervising the ballot.

The intercepts show the key officer running the militia in East Timor, Major-General Zacky Anwar Makarim, was ready to assassinate Guterres if he changed sides after the vote.

One intercept indicates that just after the arrival on September 20 of the international security force led by Australia's Major-General Peter Cosgrove, the covert campaign chiefs had sent in hit squads of special forces troops, code-named Kiper-9, to target independence leaders and turncoats from the pro-Indonesian cause.

The unfinished story of accountability in East Timor hangs over moves by the United States and Australia to improve contacts with Indonesian military and security agencies to pursue their campaign against terrorism.

The retired general Hendropriyono, who as transmigration minister in 1999 helped set up the camps into which East Timorese deportees were driven, was recently made head of Indonesia's National Intelligence Body.

On his visit to Jakarta last month, the Prime Minister, John Howard, accepted an Indonesian proposal to step up intelligence exchanges with this agency.