Naval lawyer Martin Toohey today continued his criticism of Australia's spy agency the Defence Intelligence Organisation (DIO), saying it was politicised and misled the public.

Captain Toohey has attacked the Federal Government over its treatment of him and whistleblower Lieutenant Colonel Lance Collins amid allegations of failures by the DIO.

He said he believed the Government was involved in a cover-up over the Collins affair and said he wanted to appear at a parliamentary inquiry into the military justice system.

Lt Col Collins, chosen by defence chief General Peter Cosgrove to oversee intelligence in East Timor, was at the centre of allegations he leaked sensitive material.

But a report by Capt Toohey cleared him of the claims and found evidence of a pro-Jakarta lobby within the DIO.

The Government later released another report by Colonel Richard Tracey which discredited the Toohey report.

Capt Toohey said he disagreed with the Government and said the Tracey report was a cover-up.

He said the DIO was "misleading the Government and the people of Australia".

Capt Toohey said the politicisation of the DIO was life threatening and the head of the organisation should be sacked.

"I believe that the head of DIO is politicised, I believe that he really should be replaced," he told ABC Radio. "DIO has been politicised and that is a very sad situation and indeed a dangerous situation if we have another East Timor where the intelligence is of such a poor standard again lives will be at risk."

Capt Toohey said he wanted to testify before a parliamentary inquiry because the cover-up was a constant thorn in his side.

He also claimed to be the victim of a witch-hunt for the leaking of the Collins report to the media.

"I've had two investigators from the defence security interview me," Capt Toohey said.

"I have no idea how it was leaked, I told them so. They didn't appear to have any authority to be there. It was a witch-hunt and don't shoot the messenger."