Marianne Kearney, Jakarta – Jakarta's East Timor trials were supposed to be the place where Indonesia would prove that its military had reformed and could no longer escape punishment for human rights abuses.

Instead, the trials of those who instigated the bloodshed at the time of the East Timorese referendum in August 1999 have become a chance for the military to yet again rewrite history by claiming that the violence which destroyed the province three years ago was the result of warring Timorese civilians and that the armed forces were helpless to stop it.

Yesterday's conviction of the former militia leader Eurico Guterres, along with a three-year sentence for Timor's former governor, Abilio Soares, in July, makes them the only two people, both civilians and Timorese, to be convicted of any crimes against humanity for the 1999 violence.

And this fits perfectly with the Indonesian military version of what happened in East Timor in 1999 – the violence was just a conflict between pro- and anti-independence Timorese factions, not something that they had masterminded and directed.

Throughout the trials, which have seen the acquittals of six security personnel, including a former police chief, and military officers accused of ordering the massacre of up to 150 people – according to Church estimates – in a church in the East Timorese border town of Suai on September 6, 1999, defendants have said that they were powerless to stop the violence.

Although the attorney-general's office has been provided with comprehensive evidence from an Indonesian investigation, as well as from United Nations prosecutors, proving that the militias were created, trained and backed by the military, prosecutors have used little of this.

Instead of constructing a case to prove that the massacres, and the forced removal of 250,000 people into West Timor, were orchestrated by the military, the prosecution has only tried to charge the police and military with the failure to stop violence.

This skewed evidence reinforces the Indonesian military's original propaganda about why they invaded East Timor in 1975 – to stop a violent civil war.

There are still several other military and police personnel whose trials continue, but given the acquittals of the other military officers in August, nobody expects them to be found guilty.

Analysts say there has been little focus on reforming the military since President Megawati Sukarnoputri took office last year, and this is illustrated in the Timor trials, which were supposed to show that the military could be held accountable for atrocities. "Reform in the military is dead now," said one Western analyst.