Amnesty International slammed Indonesia's trials of suspects in the 1999 East Timor violence as "not honest, truthful or fair" and urged the United Nations to consider setting up a tribunal.

The human rights group, in a report, reminded the UN of its responsibility to ensure that perpetrators of crimes against humanity before and after East Timor's bloody breakaway from Indonesia are brought to justice.

"The trials conducted by Indonesia have not been truthful, honest or fair," the London-based group said. "It is now time for the UN to find alternative ways to ensure that justice is delivered in an effective and credible process".

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.

Amnesty recalled that the UN Security Council and the UN Commission on Human Rights had demanded that offenders be brought to justice. But 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. Two generals are still awaiting verdicts.

Amnesty said indictments were weak and failed to address the role of the Indonesian military in setting up and supporting the militias. Most defendants were charged only with failing to prevent atrocities rather than direct hand in them.

Prosecutors were drawn from the attorney general's office, "which is widely acknowledged to be among the most corrupt of government departments." Crucial evidence was not called and prosecutors, according to one expert, appeared to be "acting out a role" and avoiding key issues. Amnesty said UN-funded prosecutors in East Timor, by contrast, have indicted more than 230 people including high-ranking Indonesian officials. But Jakarta has refused to hand anyone over for trial.

Amnesty urged the Security Council to launch an independent review of legal proceedings in both Indonesia and East Timor. This should consider options including strengthening the process in East Timor, an ad hoc tribunal set up by the Security Council and trials in third countries.