The head of Indonesia's Supreme Court has hit out at Amnesty International for describing trials of suspects in the 1999 East Timor violence as "not honest, truthful or fair." "That group has never been satisfied with other people's work," Bagir Manan was quoted by the Koran Tempo daily as saying.

Manan said Amnesty's criticism should not be taken seriously. "The idea that human rights courts must not acquit defendants is not true. If [the defendants' guilt is] not proven, what can you do?" he said.

Amnesty, in a report issued on Tuesday, urged the United Nations to consider setting up a tribunal to try the atrocities that took place before and after East Timor's breakaway from Indonesia. "It is now time for the UN to find alternative ways to ensure that justice is delivered in an effective and credible process" the London-based rights group said.

Pro-Jakarta militiamen organised and directed by the Indonesian army waged a campaign of intimidation before East Timorese voted in August 1999 for independence, and a scorched-earth revenge campaign afterwards. At least 1,000 people are estimated to have died – Amnesty says 1,300 – and whole towns were burnt to the ground. The UN held off on an international tribunal following Indonesian assurances that it would try offenders itself.

A special human rights court, in widely criticised verdicts, has acquitted 10 security force members and a civilian. Five people have been ordered jailed but only one has received the minimum 10-year sentence mandated by law. All are free pending appeals.

Amnesty said indictments were weak and failed to address the role of the Indonesian military in setting up and supporting the militias.