Hamish McDonald – A secret report for the Indonesian Government makes it clear that its military directed the militia violence against East Timor's independence vote and that top generals approved of some of the worst atrocities.

The 41-page report, by the Commission of Investigation into Human Rights Violations, sheets home ultimate responsibility to the then armed forces commander and defence minister, General Wiranto.

The report, marked "Secret" and "Only for the Investigation Purposes of the Attorney-General's Department", has been obtained by the Herald.

It details how the militias were trained, paid from government budgets, given modern firearms, allowed to use military bases and transport, and how the militias then worked closely with army and police units to track down, torture and kill independence supporters. Among examples detailed are: The massacre of unarmed refugees in the church grounds at Suai on September 6, 1999 which, it says, was directed by the local bupati (administration chief) Colonel Herman Sedyono, and local military commander First Lieutenant Sugito.

The reprisal execution of six independence supporters, including three school teachers, at Bobonaro on April 13, 1999 by militias directed on the spot by district military commander Lieutenant-Colonel Burhanuddin Siagian and a senior militia leader, Joao Tavares.

The massacre of at least 50 civilians in the Liquica church on April 6 by Besi Merah Putih militias, who fraternised with local army and police before and after the killings. A Police Mobile Brigade platoon stood by as the massacre took place. Army personnel helped hide the bodies.

The operational commander of the systematic militia campaign was Major-General Zacky Anwar Makarim, ostensibly in East Timor to liaise with the United Nations mission running the ballot.

The inquiry also cites: Reports sent by General Wiranto and the Bali-based regional commander, Major-General Adam Damiri, to the then security co-ordinating minister, General Feisal Tanjung, as indicating full awareness of the militia strategy. General Damiri is quoted telling General Tanjung that the Liquica massacre had made pro-independence youth "unable to act". He had told him a similar rampage by Aitarak militia at the Dili house of independence figure Manuel Carrascalao, whose son was among 15 killed, had made East Timorese "love the Red and White [Indonesian flag]" and realise that continued integration "had many supporters".

It is believed only a few copies of the report are being closely held by the Indonesian Attorney-General, Mr Marzuki Darusman.

On General Wiranto's role, the report does not include him on the list of 32 army and police personnel, civilian officials and militia members listed as suspects in crimes against humanity, including generals Damiri and Zacky Anwar.

But it concludes that the "whole range" of wide and organised violations of human rights before and after the ballot was "fully known to and realised by the armed forces commander General Wiranto", who was also in charge of the Indonesian police at the time.

"All the crimes against humanity in East Timor, direct or indirect, took place because of the failure of the armed forces commander to guarantee the security of the implementation of the two options [the ballot] proclaimed by the government," it says.