Karen Michelmore, Jakarta – East Timor's United Nations-sponsored vote for independence was a fraud, Dili's former mayor and alleged militia organiser said today.

Domingos Maria das Dores Soares accused the world body of "hypocrisy, cheating and collusion" in the August 1999 referendum which offered East Timorese a choice between autonomy within Indonesia, or independence from it.

Soares, a former district head and alleged organiser of a pro-autonomy militia group, was speaking at the landmark second public hearings of the East Timor Indonesia Commission of Truth and Friendship (CTF) in Jakarta today.

"I can read from the actions of this administration, most of them were Australians, stating the case for the plan to force one alternative – that is independence at all costs," Soares said.

The CTF is holding public hearings as its seeks to establish a conclusive truth about the violence surrounding East Timor's 1999 vote.

About 1,500 people died when pro-autonomy militia, backed by Indonesia's military, went on an arson and killing spree.

At the previous hearing, Indonesia's former foreign minister Ali Alatas said he did not believe there had been significant fraud in the 1999 vote.

But Soares said the widespread violence that followed was evidence it was unfair, adding he still felt anger.

"(Those) who conducted the referendum with fraud, they caused everything that has happened," he said. "If the referendum had been won by the majority of citizens... it would have been strange if the minority created so much unrest and destruction."

Nobel Prize laureate and former East Timor Bishop Carlos Belo also today recounted his experience during the chaos, including the attack on his own residence two days after the result was unveiled, September 6, 1999.

Bishop Belo said he was inside when militia started shooting and throwing molotov cocktails at his windows, and was soon evacuated to the residence of the police chief Timbul Silaen.

"There were shots from outside 'get out,' get out'," Bishop Belo told a packed conference room at a Jakarta hotel.

"I saw glass was shattered and scattered on the floor. I heard molotov cocktails hitting the windows and the doors."

He said he took a bottle of water from the fridge to try and douse the flames, but failed.

"The young people (in the room) were yelling Mr Belo get down on the floor... if not you will die," he said. "The flames were spreading so fast, all the way to the ceiling."

Four people are believed to have died in the attack, and Silaen was later acquitted of crimes against humanity and failing to control his subordinates carrying out the attack, at a human rights tribunal hearing in Jakarta in 2002.

Bishop Belo said when he arrived at Silaen's house, the police chief said he was "acting on orders from above". "I was told by the police chief Timbul Silaen that all was ordered from the superiors," Bishop Belo said.

"(The police chief said) 'We had to do that because the people, if there is something, they always run into the church. They have to learn not to go to the church but to look to the government'."

Later, under questioning, Bishop Belo declined to elaborate on the remark.

The commission will hear from 18 witnesses this week, including former Indonesian president BJ Habibie in a closed session tomorrow.