Fairfax Media revealed on Wednesday the story of the former ASIO operative who lost his job over a romance with a foreign national, whom he later married, and now looks set for a showdown in the Federal Court.

Greens senator Scott Ludlum said on Wednesday the situation of the former agent, who cannot be named for legal reasons, was the latest example of ASIO secrecy taking precedence over workplace rights.

The intelligence agency has dismissed its former employee's claims that he and his colleagues are denied basic appeal rights if they are stripped of their top-secret clearance or threatened with losing their jobs.

The West Australian senator said his party had long been worried about workplace rights at ASIO.

"The darkness that covers the entire operations of ASIO, from work rights to the cafeteria menu, is disproportionate to any potential security threat," he said.

"The Greens have real concerns for the workplace rights of ASIO staff. If there is any abuse of workplace rights, bullying or discrimination, there are no public avenues for complaint.

"If they did go public, they will face the full force of the law.

"Without public access to expose the lack of procedural fairness provided to employees, workplace rights can be abused and this undermines the integrity of our security agencies."

The Greens have also been critical of exemptions given to security agencies from new whistleblower protection laws, arguing the loopholes left the nation's spies above the law.

"When we were fighting to remove ASIO's blanket exemption from whistleblower legislation in June, it became clear to us just how poor any work appeals processes are available for intelligence agency staff," Senator Ludlum said.

"By denying an employee's right to publicly expose workplace wrongdoing occurring within ASIO, it makes our intelligence organisations the most vulnerable of all our public sector agencies because these are the workplaces where wrongdoing is least likely to be detected."