Jakarta – A UN legal investigator looking into Indonesia's judiciary added his voice on Friday to criticism of how the trials into East Timor violence in 1999 were being handled.

But United Nations special rapporteur Param Cumaraswamy declined to specify the problems he had raised in a meeting on Friday with Indonesian Attorney-General Muhammad Abdul Rachman.

"There are some concerns and I discussed these with the attorney general ... but it's not my place to comment at this stage," Cumaraswamy told reporters.

A new human rights court in Indonesia began its first trials this year into the violence that racked East Timor after it voted to split from Indonesian rule in a UN-sponsored ballot in 1999.

The United Nations has estimated more than 1,000 people died at the hands of pro-Jakarta militias, backed by the Indonesian military.

The international community has pressed Indonesia to punish those responsible but leading rights groups have branded the trials a farce, sceptical they will lead to any convictions.

A key criticism has been the failure to try General Wiranto, Indonesia's military head at the time of the East Timor violence.

Cumaraswamy, who arrived in Jakarta on Monday for a 10-day visit, believed Indonesia was not making an effort to consider all the evidence, a senior official at the attorney general's office said.

"He said ... we are not doing our best on a couple of things like the court is not using evidence submitted by UNTAET, which actually we are," said Haryadi Widyasa, referring to the UN Transitional Administration in East Timor which ran the territory after the vote until formal independence in May this year.

Cumaraswamy will look into judicial corruption and the independence of the judiciary before reporting to the UN Human Rights Commission in April.

His trip comes amid several court cases against high profile Indonesians and concerns by independent lawyers over a perceived lack of genuine legal reform for a judicial system critics say favours the rich and powerful.

The legal system has been criticised over issues ranging from lack of transparency to unpredictability. It faced fresh criticism last month after a controversial bankruptcy ruling against the country's fourth largest life insurer, Manulife Indonesia.

Parent company Toronto-based Manulife Financial Corp (MFC.TO) had said bribery influenced the ruling by the Jakarta Commercial Court on June 13. Indonesia is investigating the allegations.

Indonesia's Supreme Court last week overturned the Manulife ruling but some foreign investors say they remain worried by a lack of legal certainty.