Tom Allard – The Indonesian Foreign Minister told his Australian counterpart, Mr Downer, as early as February that Indonesia was arming pro-integration groups.

According to an article in the Bulletin magazine, the Indonesian Foreign Minister, Mr Ali Alatas, told Mr Downer arming of the groups was "legitimate".

Soon after, Mr Downer told the Portuguese Foreign Minister, Mr Jamie Gama, a peacekeeping force "per se" was not wise ahead of the ballot. Instead a UN presence along the lines of the Unamet mission was more appropriate.

Responding to the allegations, Mr Downer said yesterday Mr Alatas had not referred to militias but "auxiliaries found right across Indonesia" which supplemented "under-resourced police and military personnel".

Two weeks after the February meeting, Mr Downer said publicly that Mr Alatas had told him it "wasn't happening, that they weren't arming paramilitaries".

The Secretary of the Department of Foreign Affairs and Trade, Dr Ashton Calvert, and a First Assistant Secretary of the Department of Prime Minster and Cabinet, Mr Peter Varghese, had also argued against peacekeepers during meetings with US officials.

Dr Calvert told a senior US State Department official, Mr Stanley Roth: "Australia had not sensed any broad international appetite for a large-scale UN intervention." Mr Roth then warned: "East Timor is about to descend into internecine violence."

Interviewed on the ABC's The 7.30 Report last night, Mr Downer said Dr Calvert and Mr Varghese did not rule out peacekeepers "for a worst-case scenario".

"Australian planners were giving close attention to that, including the possibility of military deployment," he said. "And it ended up Roth agreed the Australian approach would keep a wide number of options open and did not preclude the peacekeeping possibilities."

By June, however, Australia had sent the Vice-Chief of the Defence Force, Air Marshal Doug Riding, to Jakarta to complain about Indonesian involvement "at the highest level" in arming and organising militias.