Mark Colvin: More details, meanwhile, are emerging about the character of the intelligence officer at the centre of the calls for a royal commission and the battle he fought within the Defence Force against claimed bias and intimidation.
PM has obtained details of a reference which General Peter Cosgrove apparently wrote for Lance Collins after the two served together in East Timor.
In the reference the then Chief of Army says Lance Collins has "excellent analytical capability", is an "inspirational leader" and is a "very honest, moral and loyal person with excellent discretion and tact."
Tonight, though, the Defence Minister Robert Hill says General Cosgrove was so concerned about the investigation into the Collins' complaint by Navy Captain Martin Toohey that he sought further legal advice.
The Minister says that advice found the inquiry had miscarried because it was conducted without proper jurisdictional authority. The matter has now been referred to the new Inspector General of Intelligence and Security for examination. Neither Senator Hill, nor ADF Chief General Cosgrove would agree to be interviewed on PM.
Meanwhile, former military intelligence officers who worked with Lance Collins, both in East Timor and here in Australia, have gone public, both to defend his integrity and back his calls for a royal commission into Australia's intelligence agencies. Matt Brown reports from Canberra.
Matt Brown: Lieutenant Colonel Lance Collins has won strong backing from former colleagues, and in the past, it appears, the Chief of the Defence Force.
Andrew Plunkett, the former regimental intelligence officer with Australia's special parachute regiment 3RAR, worked for Lieutenant Colonel Collins during the Australian military's bloody and dangerous mission in East Timor in 1999.
Andrew Plunkett: And he struck me as, you know, one of our best and brightest. You know, a brilliant mind and very good analytical skills and ah, it'd be a shame through all this if we were to lose such a good mind.
Matt Brown: This praise is reflected in a reference the then Chief of Army, Lieutenant General Peter Cosgrove wrote for Lance Collins after the two served together in East Timor.
PM is still trying to check the details with the Department of Defence but the general is presently on leave. The reference says "Lance Collins is very intelligent, perceptive and quick. He has excellent analytical capability and moves quickly to the core of an issue. He is an inspirational leader, and is a very honest, moral and loyal person with excellent discretion and tact".
So the man calling for a royal commission into the intelligence services has a pretty good looking CV, and Andrew Plunkett says a royal commission is essential to root out a pro-Indonesia lobby in defence intelligence and a general bias in the intelligence community favouring the policy of the government.
Plunkett: Anything else, anything less is a whitewash, an absolute whitewash, and of course, the government doesn't want anything that could be critical of it, however it's in the national interest.
Brown: The Head of the Australian Defence Association, Neil James, is reserving judgment on the current secret inquiry into Australia's intelligence services, but he fears it will prove unsatisfactory.
Neil James: It's likely in the long term that the only thing, I think, that will bring reform and satisfy the public interest will be a royal commission.
Brown: Neil James says the Collins affair has exposed the need for serious reform.
James: Let's face it, in the struggle against trans-national terrorism, intelligence is absolutely vital and to think that even in this day and age there are complacent and in some cases incompetent middle and senior managers in some of the agencies, it's just nothing short of a national disgrace.
Brown: But the former head of the International Policy Division in the Department of Defence, Allan Behm, says calls for a royal commission are going too far.
Allan Behm: Oh, I think a royal commission would be a total waste of the taxpayers' money at this point. The Government has given plenty of thought to the national intelligence arrangements and I think that the structure that's in place at the moment is appropriate to our circumstances as they are now.
Brown: Allan Behm says the analysis produced by one intelligence officer can be challenged or changed by those with a broader view, but that doesn't mean organisations like DIO are telling the Government just what it wants to hear.
Behm: I don't think that intelligence produced from further down the structure is distorted as it goes up to government, but I do think that it is mediated by having to take account of the very broad range of policy options that government always has before it.
Brown: Allan Behm does say, however, that the independence of the Australian intelligence community needs to be strengthened.
Behm: It also needs a government that is not going to use it as some kind of political tool, as we saw happen over the last couple of weeks, that the independence of the agencies has got to be respected because without that you don't retain that critical ingredient that government and the intelligence agencies must have, which is trust between the two sides.
Brown: This affair hasn't just provoked debate about a litany of Australian intelligence failures and problems within the intelligence community. It's exposed a troubling turf war being waged between senior Defence intelligence officials in Canberra, and military intelligence officers on the ground, like Lance Collins.
In 1998, when Lance Collins wrote an intelligence estimate warning of the likely violence Indonesia's armed forces would unleash when East Timor voted on independence, he also openly criticised a pro-Indonesian bias in the Defence intelligence community, maintained by a group of senior officials dubbed "the Indonesia lobby".
Allan Behm's department wrote back. Mr Behm doesn't remember the letter, but it cautioned against producing that sort of material again.
Behm: Look, the word Jakarta lobby has been around for at least 30 years, and I'm yet to determine exactly what the Jakarta lobby is.
Brown: According to the Toohey Report, published in the Bulletin magazine and disputed by the Government, the Head of the Defence Intelligence Organisation, Frank Lewincamp, "became so frustrated with the activities of Lieutenant Colonel Collins during Interfet that he caused the flow of intelligence to East Timor to be suspended for approximately 24 hours." Andrew Plunkett, then on the ground in East Timor, says any disruption was unforgivable.
Plunkett: In reading the investigation by Captain Toohey, what DIO has done, while we were deployed with Interfet, was cut off our access to intelligence on West Timor, and higher up, on TNI, the Indonesian Military, putting our lives at risk for the period that it was cut off, for just political reasons in Canberra.
Brown: The Head of DIO, Frank Lewincamp, has been unavailable for comment.
Mark Colvin: Matt Brown.