Inspector-General of Intelligence and Security Ian Carnell says he has no doubt that Australian troops in East Timor have been deliberately cut off from top secret information.

The claims were first made by army whistleblower Lance Collins in a series of allegations he made about the Defence Intelligence Organisation (DIO).

Mr Carnell last year conducted an inquiry into the claims and presented the report to the government in November.

Mr Carnell's predecessor Bill Blick conducted an initial assessment into the allegations, including claims officials intentionally damaged Lt Col Collins' career by spreading malicious rumours after he upset DIO director Frank Lewincamp with his criticisms of the organisation.

There were also suggestions Mr Lewincamp's dislike of Lt Col Collins had caused the flow of intelligence to East Timor to be suspended for 24 hours.

Mr Blick's May 2003 report found Lt Col Collins' concerns were sincere, but did not stand up to objective scrutiny.

Mr Carnell was asked to conduct another inquiry into the claims after he found that Mr Blick's investigation was comprehensive but not exhaustive.

During a Senate estimates hearing, Mr Carnell said he had no doubt about the authenticity of Lt Col Collins' allegations that intelligence to East Timor was purposely disrupted.

"There is no doubt as a question of fact that the access was deliberately denied," he said.

"I was able to ascertain who did the transactions and who gave that person a direction to do it.

"That persons actions I canvass in the report and also question whether have they themselves received direction from others but didn't feel that there was a case for saying they had received clear direction to do it."

Mr Carnell also told the hearing he had discussions with Mr Lewincamp before the final release of his report.

Asked if he amended the report after feedback from Mr Lewincamp, Mr Carnell said: "Yes. He had some valid points and I took them into account."

"If you're sitting there concerned that I rolled over and was softer on him. No."

Mr Carnell said he was satisfied with the steps Defence was taking to implement the recommendations of his report.

In December, Defence Minister Robert Hill said he could not release Mr Carnell's report because "for reasons of natural justice it is not appropriate to release (it)... at this time".

"The secretary (of Defence) is pursuing legal and administrative issues arising from the report," he said at the time.

Senator Hill said the defence secretary was working on those issues and an outcome was likely soon. "I understand that's not expected to take much longer," he said.

However, Senator Hill prevented questions on whether action was being pursued against current or former defence officers. "I believe providing further details on that aspect at the moment would infringe the rights of individuals," he said.