Secretary-General Ban Ki-moon has told UN officials not to testify before a panel investigating the 1999 killings in East Timor because it could recommend amnesty for serious crimes. Indonesia and East Timor agreed to work together to investigate the events of 1999, when Timorese voted for independence under UN supervision.

The two countries have organised a Commission of Truth and Friendship to try to put the tragedy behind them.

Riots blamed on militia, backed by the Indonesian army, killed many Timorese, forced 250,000 people from their homes and burned most buildings to the ground in the former Portuguese colony.

Indonesia says only about 100 people were killed before Australian troops stopped the mayhem, followed by a UN peacekeeping mission.

Ban said the commission was allowed to recommend amnesty, even for serious crimes.

"The United Nations' policy, however, is that the organisation cannot endorse or condone amnesties for genocide, crimes against humanity, war crimes or gross violations of human rights, nor should it do anything that might foster them," Ban said in a statement.

"Unless the terms of reference are revised to comply with international standards, officials of the UN will therefore not testify at its proceedings or take any other steps that would support the work of the CTF," he said.

Among those called to testify is Ian Martin, who was the UN special representative in East Timor in 1999. He is now the UN envoy in Nepal.

Both Indonesia and East Timor have set up parallel systems to prosecute those responsible but UN reports have described those efforts as inadequate. The commission cannot prosecute but its hearings are likely to have an impact on the Indonesian public and government.

Militia leader Eurico Guterres, the only person jailed in Indonesia for the violence, is serving a 10-year sentence.

Human Rights and Timorese victims groups have harshly criticised the commission for not challenging witnesses and cross-checking facts. They say the truth was being distorted, particularly by those blaming the United Nations for inciting violence when it organised the independence referendum.

East Timorese voted overwhelmingly to split from Indonesian rule. The 1999 referendum was made possible, in part, by the fall of Indonesian strongman Suharto a year earlier, who had the support of the military.