Catharine Munro, Jakarta – Indonesia began landmark trials focused on human rights abuses in East Timor yesterday, with two high-ranking officials answering charges of crimes against humanity.

But doubts were immediately raised as to how far the cases would proceed when defence lawyers announced they would call on the country's highest legislature, the National Assembly (MPR), to review the validity of the tribunal.

East Timor's former governor, Abilio Soares, 54, and its then chief of police, Timbul Silaen, 53, were accused in separate hearings of crimes against humanity.

"The defendant conducted gross violations of human rights by failing to secure peace and order and failing to control widespread and systematic attacks on the civilian population and being unable to control subordinates committing gross violations of human rights," Silaen was told.

Soares faced the same allegation, but while the police chief was accused of failing to control police, the governor was responsible for militia gangs who had been ostensibly set up to maintain security ahead of the poll. Both denied the charges, which could carry the death penalty.

Nearly 1000 people were killed and most of the territory's infrastructure was destroyed after the 1999 vote to secede from Indonesia sparked violence that was aided and abetted by the security forces. The two officials are the first of 18 suspects to appear before the court.

Soares's defence lawyers said they would lodge judicial and legislative appeals on Monday that questioned the validity of the court. The MPR Speaker, Amien Rais, who is a key political player, would be called upon to judge whether the laws that enabled the court to be established conflicted with sections of the Constitution. "It is up to him [Rais] to decide the legality of the ad hoc tribunal," a defence lawyer, Indriyanto Seno Adji, said. The Constitution was recently amended to prevent laws being applied to incidents that occurred before those laws existed.

Human Rights Watch's Asia director, Sidney Jones, said that along with the constitutional amendment the defence had a number of legal avenues to pursue to ensure that the tribunal could not complete its work. "I don't know what will happen with the [defence] appeal per se but even if it doesn't proceed ... I can't believe we are going to see any real justice being done," she said from New York.

The court is yet to charge the other two generals on the list, along with a string of low-level commanders and militia gang leaders.

Nearly 200 demonstrators opposed to East Timorese independence marched into the court grounds, chanting anti-Australian and anti-Portuguese slogans, and many entered the courtroom to support the defendants. "It's not fair," the East Timorese leader of the Aitarak militia, Eurico Guterres, said. "If the court wants to investigate us, it should investigate other cases."

President Megawati Sukarnoputri limited the scope of the human rights tribunal to events that occurred in April and September 1999, a measure that has been criticised by human rights groups.