Australia's mandatory detention of boatpeople is to come under fresh legal scrutiny with a refugee advocate unveiling a High Court challenge to government security checks of detainees.

Lawyer David Manne, who succeeded in having Canberra's so-called people-swap deal with Malaysia struck down by the High Court last year, said he was preparing a new case against the government's mandatory detention policy.

Manne said on Thursday he was challenging secret assessments conducted by the Australian Security Intelligence Organisation (ASIO), which have seen detainees found to be genuine refugees remain behind bars because they are deemed a threat to the community.

"It is like a secret trial. We don't know the process, we don't know the rules," Manne told the Australian Broadcasting Corporation.

"All we know is the negative outcome and the consequences, and the consequences are cruel."

The challenge will focus on the case of a Sri Lankan man who has been locked up for more than three years after receiving an adverse ruling, but does not know why.

A spokesman for Immigration Minister Chris Bowen declined to comment on the specifics given the matter was now before the court, but said security reviews were a key part of the asylum process.

"These are complex cases, but the government cannot compromise on matters of national security," the spokesman told AFP.

"Of course, we ensure appropriate arrangements are in place for the care and support of people detained due to an adverse security assessment."

There are some 50 genuine refugees, including a pregnant mother and her children, who remain in detention on security grounds and Manne said it was a denial of natural justice to lock them up "indefinitely and possibly forever".

Australia had to relax its refugee policy after the High Court declared invalid its plan to send 800 boatpeople to Malaysia in exchange for 4,000 proven refugees, a ruling that also scuttled its offshore processing plans.

Thousands of asylum-seekers have since been released into the community to await their visa ruling in a bid to relieve pressure on detention facilities as a steady stream of people-smuggling boats continue to arrive from Asia.