Karen Michelmore, Jakarta – The former head of Indonesia's armed forces has conceded that "one or two" of his men may have been involved in the bloodshed that swept East Timor in 1999.

But retired General Wiranto staunchly denied any gross human rights violations occurred in East Timor before and after its historic 1999 vote for independence. Instead, he blamed the carnage on a long-running internal conflict inside East Timor.

Wiranto – who was indicted by the Dili Special Panels in absentia in 2003 for alleged crimes against humanity and was a presidential candidate in Indonesia in 2004 – today testified before a commission investigating the 1999 violence.

"These were only the actions of elements (of the military)," Wiranto told the East Timor Indonesian Commission of Truth and Friendship (CTF) sitting in Jakarta.

"It was not based on orders. This was not planned, this was just personal behaviour. This is just individual responsibility. The Indonesian military didn't take any sides."

The CTF was established by the presidents of Indonesia and East Timor to come up with a "conclusive truth" about the violence that swept East Timor in 1999 to help the nations reconcile.

However, the CTF, which favours friendship with Indonesia over prosecution, has been criticised by human rights groups concerned it will recommend amnesties for alleged perpetrators of human rights abuses and cloud the history of the violence.

Numerous investigations have found up to 1,500 people were killed, hundreds of thousands of people were displaced and about 70 per cent of the nation's infrastructure razed when militia groups linked to the Indonesian security forces rampaged across East Timor before and after the historic vote.

Wiranto said the Indonesian security forces had a difficult job of securing the 1999 ballot within just three months because there had been a "horizontal conflict" in East Timor for decades.

He said the ballot itself had been a success and the violence after it was because the losing side was concerned about the legitimacy of the vote.

Wiranto said pro-Indonesia groups told him on September 5, 1999, they wanted to burn down East Timor after losing the ballot, but he told them not to.

"They said to me: 'Mr Wiranto, we have lost and we will destroy all the facilities that Indonesia has built'... (but) I said: 'No, don't ... people need these facilities'," Wiranto said.

He told the group they would be "demolished" if they tried to raise the Indonesian flag and continue fighting, because it was against the wishes of the international community and the decision of Indonesia.

"There was no instruction, no plan, no support for the destruction, for the arson," Wiranto said. He denied he had control of the militia group, or even direct control of his subordinates who may have been involved in the violence.

"Does a commander really know what their direct subordinates would do?" he said.

He said the incidents of violence were "common crimes" and not gross violations of human rights because there was no order from above of state plan behind the bloodshed. However, he said he had resigned as minister of defence because of his "moral responsibility" for the violence.