Riding the twin horses of America and China is difficult for Australia and will be more so as the US seeks to contain China, with what it has been led to believe, by policy makers and junkies of the Australian/American Leadership Dialogue and right wing ''think tanks'', is Australian support and compliance.

Understandably the Indonesian military are uneasy, watchful, and increasingly tetchy at these developments. Putting a Brigade of deployable, combat-ready Marines and US Naval vessels into Darwin, basing B52s at Tindal, home porting US submarines at HMAS Stirling in Western Australia and flying US unmanned spy aircraft out of Cocos Island have combined to cause concern. This concern has been officially and unofficially expressed; Cocos sits in the lee of Indonesia. Unofficial expressions of concern have come from a range of contacts and from listening to Indonesian conversations from Australian facilities and from the Joint US/Australian communications base at Pine Gap, where about 1000 US National Security Agency, and Central Intelligence Agency personnel carry out a range of surveillance activities, including tapping phones and other communications using Echelon, a sophisticated and effective listening system.

During the brutal Indonesian occupation of East Timor, Australia monitored military communications. It was well aware of military operations against the Timorese resistance. Indonesian casualty reports of deaths and injuries to both sides were intercepted.

They detailed genocide. Within my responsibilities as director of the Indonesia section I had the call as to whether the minister, Bill Hayden, should be sent these weekly reports. I chose to send them.

One day an operative from the security branch of the department came to me and said that there was ''thinking'' that it might be better and less time consuming for the minister if he were to receive a six-month summary of the information. Apparently it was information overload for the hard-pressed man. I thought not and said so. I felt it was important for the minister to be up to date with the activities of the military of a neighbouring country we refused to criticise publicly and privately over genocide. So the minister received his weekly dose of regional horror, but I don't know whether he read it, there was no feedback.

In the run into the reluctant intervention in East Timor, Australian intelligence agencies were keen to distance themselves from the churlishness of Howard and Downer. Members of this community briefed journalist Paul Daley in March 1999. Writing in The Age of 20 March he said that the Australian Secret Intelligence Service and the Defence Signals Directorate were working around the clock monitoring signals into and out of East Timor. Daley also said that a massive reconnaissance effort including the help of US spy satellite stations in Australia was underway to prepare maps and photographs of Indonesian military installations.

An academic, Associate Professor Clinton Fernandes, of the University of NSW, several years ago put in an FOI request to the Department of Foreign Affairs for documents relating to Australian government knowledge of (and therefore complicity in) the mass starvation of East Timorese in 1978-79 as an instrument of Indonesian military control. Quite rightly Fernandes is seeking documentary evidence of a shocking event which saw about 100,000 people die out of a population of 640,000. A further 100,000 East Timorese died as a result of the armed struggle, detention, torture, rape and relocation during the occupation.

Fernandes says the documents relate to cables written by the Australian embassy in Jakarta. From my own knowledge they report information from visitors to the island, East Timorese living and studying in Jakarta, the Red Cross (although not named as a source), members of the Catholic Church both local and overseas and NGO visitors to the island. The cables also detail forced relocation of East Timorese and the transmigration of Javanese.

DFAT has refused to release the documentary evidence on grounds of security, defence and international relations. These reasons are spurious. Attorney-General Nicola Roxon has blocked Fernandes from testing them in court.

Of course gaining access to the documents matters, but the timing is wrong (has it ever, in the eyes of DFAT, been right?). For all the old reasons of not wanting to offend the Indonesian military and its putative political masters, now exacerbated by Australia's closer embrace of the US, DFAT seeks to please. All the more so now when the new embrace involves weapons systems that are perceived as being just as easily deployed against Indonesia as China.

Rudd put the relationship, with the political and military power structures of Indonesia, under some strain as a result of attempting to push refugees in boats back into the ''care'' of Indonesia in 2009. He was seen as arrogant and crude and his departure both as prime minister and foreign minister was not lamented in Jakarta, just as it was not in Beijing.

Abbott, if he gets elected, threatens to do the same thing with his ''tow the refugee boats back to Indonesia policy''.

DFAT is acutely aware of these foreign policy shortcomings. On the other hand DFAT stands in the way of a more mature relationship with Indonesia by seeking to keep in the closet some awful truths which would do both sides far more good than harm to air and discuss.

We know what happened in East Timor. The point Fernandes seems to want to make is that at the official level both sides should acknowledge their complicity. Clear the air, start afresh - all good except that Australia appears to want closer relations outside the region than within it.

Bruce Haigh is a retired diplomat and political commentator.