Tom Allard – As an intelligence officer at Australian theatre headquarters in Brisbane, Lieutenant-Colonel Lance Collins was charged with writing highly classified reports on East Timor.

In July 1998, he wrote a chilling assessment that the Indonesian military was sponsoring militia violence and the Indonesian province was a powder-keg.

That began a stream of alarming intelligence reports as the East Timor crisis developed. The reports included warnings there could be mass bloodshed following the independence ballot that took place a year later.

Colonel Collins was admonished by Defence policy officials in late 1998 for going beyond his brief of looking only at operational matters and for failing to understand the foreign policy relationship with Indonesia that underpinned the government's stance on East Timor.

To critics this was tantamount to saying the military intelligence network had to consider political objectives. Australia then supported Indonesia's occupation of East Timor.

But the analyses were remarkably prescient and they were all but ignored by the military's top brass.

The violence that followed profoundly disturbed Colonel Collins and, frustrated by his treatment by military insiders, led to him taking the extraordinary step of writing to then defence minister, John Moore, in 2000. His comments were passed on to Mr Moore's successor, Peter Reith.

Colonel Collins accused a pro-Jakarta lobby at the highest levels of Defence intelligence of muzzling his intelligence reports and harboured misgivings about the suicide of Defence Intelligence Officer Merv Jenkins for passing on sensitive intelligence to the US.

The intelligence related to East Timor and came as the US was worried they weren't getting the full picture on the troubled province.

Colonel Collins had served for five months as commander General Peter Cosgrove's top military intelligence adviser in East Timor. But he complained that a campaign was waged against him after his return to Australia.

This culminated in the listing of his name on a federal police search warrant in August 2001. The list of names of the warrant was leaked to the media, outing Colonel Collins as a spy, an act that cruelled his espionage career.

He sought redress through the Inspector-General of Intelligence, Bill Blick. A meeting was organised with Mr Blick, believed to have been attended by Defence Intelligence Organisation boss Frank Lewincamp.

In a Kafka-esque nightmare that followed, Mr Blick and Mr Reith said they had investigated – using ASIO – supposed allegations made by Colonel Collins that there was an Indonesian agent in the high ranks of the military. But Colonel Collins said the allegation was never made by him.

A second internal inquiry was then conducted by a military legal officer, Captain Martin Toohey. Captain Toohey's report, delivered in the second half of last year was damning of the treatment of Colonel Collins, reserving some of its harshest words for Mr Lewincamp.

It recommended Colonel Collins be reappointed as a military intelligence officer, commended for his work on East Timor and considered for promotion. The matter appeared to have been finally settled. But the report was ruled inadmissable.