David Lague – Hostility towards Australia in the Indonesian military is undermining efforts to rebuild ties between Canberra and Jakarta and threatening the safety of Australian service personnel and equipment.
Indonesia's menacing interception of four RAAF FA-18 fighters and its Boeing 707 in-air refuelling tanker last week shows that this suspicion and antagonism arising from Australia's military role in stabilising East Timor could lead to a confrontation or an accident that would be damaging for both sides.
It remains unclear why the Australian aircraft were challenged if, as the RAAF says, they were in acknowledged international air space and their flight plans had been cleared by Jakarta's aviation authorities.
Similar difficulties could arise for Australian warships and submarines using the many recognised international waterways of the sprawling Indonesian archipelago. Indonesia has long sought to tighten control over the sea lanes crossing its territory.
Last week Indonesia's Foreign Minister, Mr Alwi Shihab, encouraged speculation that recent orders for Jakarta's navy to become more alert were directed at the operations of Australian submarines.
There is also the potential for confrontation in East Timor while Indonesia continues to train and arm militia in West Timor for raids across the border, where Australian troops are deployed with the United Nations peacekeeping force.
Senior Australian Army officers say that the Indonesian Army's behaviour in West Timor and along the border is far from peaceful.
Any hostile act by Jakarta, or damaging accident, particularly where air safety was involved, would be another blow to an international reputation already in ruins after its military's bloody exit from East Timor.
The Howard Government is trying to play down Wednesday's encounter, and had not bothered to inform the public until it was reported in the Indonesian press at the weekend, but the Minister for Foreign Affairs, Mr Downer, yesterday acknowledged that hostility in Jakarta over East Timor was harming ties.
This resentment is unlikely to ease in the near future if Australia is conducting covert reconnaissance flights over Indonesian territory, as some influential members of Jakarta's elite regularly claim.
Mr Downer was unable yesterday categorically to deny these so-called black flights. "I can only tell you what the RAAF and the Defence Department and the Defence Minister have told me ... that we have mounted no black flights over Indonesia," he told Channel 9's Sunday program.
Jakarta is well aware that, with vulnerable troops on the ground in East Timor, Australia's military and intelligence services are using every tool at their disposal to probe Indonesian military movements and intentions, particularly in West Timor.