Mark Colvin: One of the key claims in the Collins case is the statement by the Lieutenant Colonel that Australian Defence intelligence on East Timor was distorted by a pro-Jakarta lobby.

The term "Jakarta lobby" has a long history in Canberra and our Foreign Affairs Correspondent Graeme Dobell has been looking at its impact during the violent months surrounding East Timor's independence vote in 1999.

Graeme Dobell: The term "Jakarta lobby" was first applied to Indonesia specialists at the Australian National University in Canberra 30 years, but the claim of a pro-Jakarta mindset has just as often been levelled at Australian diplomats, especially in the agonised debate about the invasion of East Timor in 1975.

The new claim is that the Defence Department was also afflicted in the tense period surrounding the United Nations ballot in East Timor in August 1999. Professor James Cotton of the Australian Defence Force Academy on the factors underlying a pro-Jakarta habit of mind.

James Cotton: Well whichever way you look at it, Indonesia is the key country. It's the key country strategically in geographical terms. It's the core country of the South-East Asian regional organisation, ASEAN. For two generations, managing the relationship with Indonesia has been a key concern of governments of both persuasions in Canberra.

So putting another objective ahead of that particular priority is going to be a very, very difficult wrench and one suspects that some people, when confronted with this choice, simply hope for the best.

Graeme Dobell: The caution about Indonesia is evident in the history of the period published by Australia's Foreign Affairs Department, which maintains the view that it's impossible to know to what extent the militia violence in Timor was sanctioned or ordered from Jakarta.

The Foreign Affairs version is that Canberra judged it extremely likely there'd be violence after the UN ballot, but did not anticipate the sheer scale of the disaster.

The version from the Defence Department is different and hints at the Collins' frustration with a perceived Jakarta lobby. The military view, offered in a report by the Auditor-General, is that Defence had no mandate to plan for a peacekeeping operation in East Timor which did not assume Indonesian agreement. Further, the Auditor-General found Defence planning and pre-positioning of troops in Darwin, close to Timor, was constrained by diplomatic considerations.

Despite the deterioration in East Timor in the period leading up to the vote, Defence said there was no government strategic requirement for the Defence Force to be able to form or lead an international peacekeeping coalition force. Was that the narrow vision of a pro-Jakarta lobby? Professor James Cotton.

James Cotton: I mean the Government's own document on Timor policy has a number of propositions in there. It says that basically the Army high command in Indonesia, or some members of the high command, were running the militias. It says that Australia had very little prospect of changing Indonesia's policy on East Timor.

Nevertheless, Australians were put in harm's way in East Timor with the expectation, I think, that there was very little prospect other than a major upheaval with the advent of an independence vote. That's how it turned out. We were very, very lucky that no Australians were killed or injured in East Timor because this could have very easily happened.

Graeme Dobell: Does the evidence now suggest that Australia was lucky in East Timor, that there was both an intelligence and a policy failure in East Timor, before Australia's troops went in?

James Cotton: Well we know from the National Audit Inquiry of 2002 that the Defence organisation was specifically prohibited from planning for an operation of the kind that became Interfet. They were to look at some other alternatives – the extraction of international personnel, or perhaps the participation in a peacekeeping force sometime after the independence ballot, but not for the kind of operation that Interfet became.

I mean this was, in some ways, to hamstring the organisation, to prevent them from planning for the very operation that in the event occurred. So yes, the fact that it all turned out the way it did was considerable luck.

Mark Colvin: Professor James Cotton of the Australian Defence Force Academy.