The man was employed by the Defence Department as a security clearance expert and claimed he was bullied and intimidated by officers after raising concerns about allegedly unethical processes.

He held a top secret positive vetting clearance until he was placed on extended medical leave in 2010 with a review of his clearance ordered after concerns it had become inappropriate.

Court documents show the review was cancelled once he was transferred to a new role within the department, which saw his clearance automatically downgraded.

But he raised concerns the review had been handled improperly with conflicts of interest and complained to the secretary, a deputy secretary and the Inspector-General of Intelligence and Security.

He requested access to documents related to the review under freedom of information laws in 2012 but many were denied, only to be shown to him under supervision.

He contested the decision and unsuccessfully sought a full publication from the Information Commissioner. He then challenged the decision before the Administrative Appeals Tribunal but was unsuccessful.

Elizabeth Milne, an assistant secretary at the Australian Government Security Vetting Agency, told the tribunal that publishing the documents could have unintended consequences.

She said the documents could allow foreign agents to infiltrate the government as they provided details on how to rehearse psychological tests and manipulate results.

"The information contained in these documents would be of significant assistance to a person seeking to alter the result of psychological testing to allow them to appear more suitable than they may have appeared if the process had not been interfered with," she said.

The documents, according to Ms Milne, included interview questions for referees and could allow applicants with hidden intentions to game the system.

"Disclosure of these questions would pre-warn all future positive vetting security clearance subjects and their referees of the specific questions they would be asked in a referee interview and enable them to prepare their responses in advance," she said.

She said the documents would "provide an opportunity for parties with hostile interests to infiltrate sensitive government information and use it in ways which may be contrary to Australia's national interest."

AAT deputy president Stephanie Forgie made no judgment on whether the former Defence employee had been treated unfairly or bullied by department officials.

But she found the ordeal had an "immense impact on his closest personal relationships with his family and friends".

"The loss of his job has, in turn, has had a significant impact on his financial circumstances with the result that he has had to restrict and curtail his standard of living for the rest of his life due to the early termination of his working life," she said.

Comcare accepted liability for his illness in 2014.

"[He] feels that his sense of worth had been destroyed as has his standing in the defence security and intelligence community," Ms Forgie said.

"His work at the department was not just a job but a calling for him and a calling that enabled him to perform real and genuinely valuable work directed to fostering and supporting the national security of his country."