John Howard feared Indonesian rejection of East Timor independence

John Howard says there was ‘a risk’ some elements of the Indonesian military would not accept the East Timor vote.

Chief of the UN peacekeeping force Peter Cosgrove, then a major general, meets with his Indonesian counterpart major general Syahnakri. Picture: AP

On the day East Timor voted for full independence rather than autonomy within Indonesia, in August 1999, John Howard told cabinet that BJ Habibie reaffirmed Indonesian authorities would ­“ensure security and stability” in East Timor and also the “safety” of Australians there.

The prime minister’s phone call to the Indonesian president was reported to cabinet and was released­ on Wednesday by the National Archives of Australia. It also reveals Habibie was told of Australia’s “contingency arrangements” in the event that Australians had to be quickly evacuated.

In an exclusive interview, Mr Howard told The Australian there was “a risk” that some elements within the Indonesian military and government would not accept the outcome of a ballot that endorse­d independence.

“I had some concern that things might get out of control because the ballot had gone very strongly in favour of a complete break from Indonesia,” Mr Howard said.

“I didn’t think the Indonesian forces were going to take to that very kindly. You had rogue elements in the Indonesian military.

“I was really saying to him that it was the responsibility of Indonesia to ensure the peaceful transition and the peaceful implementation of the results of the ballot — whether you call that putting him on notice, it was just a statement of the Australian position.”

After Habibie flagged limited autonomy for East Timor, Mr Howard wrote to the Indonesian president in December 1998 suggest­ing “an act of self-determin­ation” following a negotiated period of “autonomy”.

Habibie seized on the letter and announced the following month that a vote would take place. Agreement on how this would work was reached in May 1999.

“Habibie had absolutely no interest in the longstanding policy of the Indonesians towards East Timor,” Mr Howard said. “He thought East Timor was a burden for Indonesia.”

There were flashpoints of violence instigated by militia groups in the lead-up to the historic vote, ­assumed to be aided by elements of the Indonesian military. ­Ac­cording to the August 1999 cabinet minute, Mr Howard flagged with Habibie “the possible deployment of a UN peacekeeping force in East Timor during any transitional phase” in the event that a majority voted for independence.

But even as more violence broke out when the result of the vote was announced in September, Habibie resisted pressure to allow international peacekeepers to assist in East Timor. Eventually, after urging from Bill Clinton, the Australian-led 22-nation ­Inter­national Force East Timor ­(INTERFET) deployed in ­September. A UN peacekeeping force took over from INTERFET in February 2000.