A former militia leader who claims the Indonesian military drugged him and gave him weapons to kill independence supporters in East Timor says the generals responsible must be held to account.

Joni Marques spent eight years in jail for crimes he committed as leader of a brutal pro-Indonesian militia, including the murder of nuns and a priest, around the time of East Timor's 1999 independence vote.

Marques claims that drugs he was fed by the Indonesians "destroyed his mind" and allowed him to join in the violence. The generals responsible must be held responsible for the devastating violence that surrounded the ballot, he said.

Marques made the call ahead of the formal release in Bali on Tuesday of a report resulting from the landmark East Timor Indonesia Commission of Truth and Friendship (CTF).

The report, which Jakarta has said it will accept, blames Indonesia for murders, rapes and torture in East Timor in 1999. It says government funds from Jakarta allowed pro-Indonesian militias to carry out coordinated attacks, and that some Indonesian army personnel played a lead role in the violence.

But it also says pro-independence groups in East Timor committed gross human rights violations, namely illegal detentions, and that Dili must join Jakarta and offer an apology.

Marques said the Indonesian generals who directed his group must pay a price for the violence that erupted at his own hands, and at the hands of his operatives.

"Those generals – the leaders who were in East Timor at the time, they must take responsibility," he said. "[The Indonesians] must take the responsibility for the victims, for the people dead. Those people died because of the weapons given by them."

Marques claims a member of the Indonesian military in East Timor fed him drugs that led him to be involved in murders. "They gave a me a capsule to take [and] that medicine destroyed my mind and I killed the nuns."

He said it took six days for the drugs to wear off and only then did he realise what he had done.

The truth and friendship commission's mandate did not make any provisions for it to recommend prosecutions, nor does the final report name the individuals responsible for the violence.

Equally, though, the report does not say that an amnesty should apply – something that could prompt fresh calls for an international tribunal or court to hear specific cases.

While Marques blames the Indonesians for his actions, he also takes a degree of personal responsibility. He points to the eight years he served of a 33-year sentence, before being handed a pardon by East Timor's President Jose Ramos Horta.

"I'm an East Timorese, so I must take the responsibility here. If they (the Indonesians) want to do over there what I have done here, it can give a good image for their country," he said. "I took a 33-year prison sentence because I did something bad, I [too] must take responsibility."