James Dunn – Jill Jolliffe's report detailing Jakarta Governor Sutiyoso's involvement in the torture of prisoners in East Timor (Canberra Times, Saturday, July 14) raises questions that go well beyond the NSW coronial search for those responsible for the Balibo murders.

It involves another troubling cover-up of Australia's support for Indonesian moves to conceal the crimes against humanity committed during those 24 years of occupation of East Timor. Australia and the United States quite shamefully failed to support UN recommendations that an international tribunal be set up to identify the military commanders responsible for very serious crimes against humanity, and the brutal culture that had developed in the Indonesian military, the TNI.

The Indonesian withdrawal in 1999 offered a unique opportunity to expose that culture and the commanders, but we were soon to learn that the humanitarian concerns of key international players like Australia, were secondary to their determination to prevent anything that would destabilise the new Indonesian regime, in which an unreformed military continued to be a main player.

Interfet forces, to the frustration of officers like Lieutenant-Colonel Lance Collins, were actually discouraged from collecting evidence of war crimes. Moreover, when I was preparing a report for the UN on the crimes committed in 1999, I got generous support from the Irish, Canadians and New Zealanders, but none from our diplomatic mission.

What I did get was encouragement from Indonesian human rights officials who declared that the full public exposure of their military's misdeeds was essential if their democratic goals were ever to be attained. One such supporter was Munir, a courageous human rights activist who was later to be murdered, allegedly on orders from Indonesia's main intelligence agency which then frustrated attempts to identify those responsible.

In the end in my view, there was a subtle cover-up. Our efforts to secure UN Security Council support for a formal investigation came to nothing, despite the helpful efforts of Sergio Vieira de Mello and Kofi Annan. The US, Australia and other influential players had other ideas.

They were against any exposure that might destabilise the restless Indonesian political scene.

In East Timor itself, the position of president Xanana Gusmao was very unhelpful. He exhorted his people to forgive the past and look to the future, denying them a measure of closure. For most, this dismissal of justice merely served to intensify the trauma that inhibits the confidence and trust of a people, whose terrible past ordeals appear to matter nothing to the outside world.

The joint truth and reconciliation commission Indonesia agreed to has turned out to be little more than a sideshow in which the Indonesian generals who have agreed to appear, have blamed the UN or the Timorese, disclaiming any responsibility for their part in the events of 1999.

For those of us who have examined or lived through the events of the past, the real situation is very different. Tens of thousands of East Timorese were killed or tortured, especially in the first five years of occupation, as part of a deliberate policy. From the outset, officers like then Captain Yunus Yosfiah and his Special Forces colleague, Captain Sutiyoso, treated those who dared to resist or question appallingly, using torture and summary executions.

Timor became a cruel military training ground, with most of today's TNI general staff, including President Susilo Bambang Yudhoyono himself, having served there.

A number of these generals have been indicted by UN prosecutors for crimes against humanity, and it is shocking to learn these indictments have in no way hampered their careers. We know about Yunus Yosfiah and Sutiyoso, but there is Major-General Tono Suratnam, now a senior headquarters general, who (then a colonel) bears a responsibility for atrocities in the Dili area.

Major-General Mahadin Simbolon, then a brigadier-general, played a commanding role in the destruction of East Timor in September 1999, and went on to command TNI forces in West Papua.

As for then Kopassus Major Prabowo Subianto, he bears a heavy responsibility for the Creras massacre in 1982, in which more than one thousand Timorese non-combatants were gunned down as a reprisal action. Then there is Lieutenant-General Sjafrei Sjamsuddin, one of the planners of the militia and its agenda of violence, who is currently secretary-general of Indonesia's Defence Department.

Not all of these officers are escaping human rights scrutiny.

Indonesian human rights agencies are calling for the removal of a sector commander in West Papua, Colonel Burhanuddin Siagian, who has been indicted for a particularly nasty atrocity in the Maliana region in 1999. However, the fact that the TNI has ignored such indictments, and the recommendation of Indonesia's own human rights commission, is an indication of how little impact its nation's shift towards respect for human rights has had on a military which, like the KGB, saw itself as a ruthless protector of an authoritarian state.

It would be unfair to blame Air Chief Marshal Angus Houston, an officer noted for his humane approach, for his intervention, for he clearly is not familiar with a background which, even in the Defence Department, is apparently being kept in the dark. As has been revealed in Balibo coronial inquiry, it is likely past atrocities by Indonesian troops in East Timor were made known by intelligence agencies to the governments of the time.

[James Dunn is a former diplomat who served as UN expert on crimes against humanity in East Timor in 2001-02.]