Alleged Timor war crimes forgotten as ministers fly in for Bali terror summit

Jakarta: The Australian Government has closed the book on war crimes in East Timor allegedly committed by Indonesia's new chief security minister, stressing it needs to pursue what is in Australia's national interest in 2016.

Justice Minister Michael Keenan and Attorney-General George Brandis will this week meet Wiranto, Indonesia's newly appointed Co-ordinating Minister for Political, Legal and Security Affairs, at a counter-terrorism summit in Bali.

Wiranto is Indonesia's Co-ordinating Minister for Political, Legal and Security AffairsCredit: Getty Images

Mr Wiranto, a former general who was Indonesia's armed forces commander during the referendum on East Timorese independence, was indicted for crimes against humanity by the UN-sponsored East Timor Serious Crimes Unit in 2003.

Human rights organisations both within and outside of Indonesia have criticised his surprise appointment in a cabinet reshuffle last month, arguing it called into question Indonesian President Joko Widodo's commitment to pursuing accountability for past human rights violations.

Justice Minister Michael Keenan says it's in Australia's national interest to have 'the closest possible co-operation with Indonesian security agencies'.Credit: Justin McManus

Justice Minister Michael Keenan told Fairfax Media he was not going to run commentary on his ministerial colleagues in other countries.

"I don't think that's particularly helpful," Mr Keenan said.

"Minister Wiranto is the new co-ordinating minister for security so Australia will seek to have a close and cooperative relationship with him.

"Our national interest is in having the closest possible co-operation with Indonesian security agencies.

As many as 2000 East Timorese people were killed in the months before and days after the 1999 independence referendum.

"We are keen to do that because more Australians have been killed in (terrorist) attacks in Indonesia than the whole rest of the world combined."

An estimated 1000 to 2000 East Timorese people were killed in the months before and days after the referendum and about 500,000 were forced to flee from their homes.

Wiranto was chief of the Indonesian armed forces in 1999.Credit: AP

The former Howard government supported self-determination for East Timor and Australia led the UN-backed International Force for East Timor to end the violence in the wake of the 1999 vote for independence.

"Australia should be very proud of what we achieved in East Timor," Mr Keenan said.

"It's a remarkable example of using our influence in the region to help in what was a very difficult situation, but we in government need to pursue what is in Australia's national interest in 2016," he said.

"It's vitally important we continue to focus on that and it is in our interest that we continue to co-operate in national security matters with Indonesia."

Nicholas Koumjian, the chief prosecutor for the Serious Crimes Unit in East Timor from 2003-2005, said future international cooperation with Indonesia had been jeopardised.

"Efforts to combat terrorism, narcotics and human trafficking require sharing intelligence and co-ordinating enforcement efforts across borders," he wrote in The Jakarta Post.

"A successful strategy requires that these battles are fought under the rule of law, respecting individual freedoms and holding police and military forces accountable for any abuse of their positions.

"Wiranto's selection sends the message that military forces are above the law and will not be held to account for past or future crimes."

Mr Wiranto has denied accusations of his involvement in past human rights abuses.

"I want [people] to clearly point out when and where exactly my involvement was. Only then will I explain, one by one," he told journalists after he was inaugurated.

The US State Department said the composition of Indonesia's cabinet was a matter for the president but it was aware of allegations of human rights violations against Mr Wiranto.

"We continue to discuss the importance of accountability for past abuses and addressing impunity within the security forces," it said in a statement.