Guterres was deputy commander of the militia groups, set up by Jakarta ostensibly to maintain security in the province.
He was also the flamboyant chief of the Aitarak militia gang based in capital Dili who threatened four days before the vote that the town would be turned into a "sea of fire" if independence was declared.
With the overwhelming vote to secede, East Timor was ransacked by militia and more than 1,000 people were killed.
Prosecutors today claimed Guterres incited an attack on the home of independence leader Manuel Carrascalao, where 136 refugees were sheltering on April 17, 1999.
Carrascalao's adopted teenage son was among 12 who died in the attack.
must be killed," he was accused of telling his supporters in a scene at the governor's office that was widely televised, Yusuf said.
But absent from the charges was any reference to allegations by East Timorese human rights group Yayasan HAK that Guterres led an attack which resulted in a massacre in the town of Liquica in the same month.
Under the Dutch-based Indonesian legal system, Guterres, who is not in detention, was not required to enter a plea.
Afterwards, Guterres, wearing a scarf with Indonesia's national colours of red and white, approached the members of the bench, all of whom agreed to shake his hand.
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