A Canberra public servant accused of spying has lost a bid to have secret information released to his legal team.

Yeon Kim had his decade-long secret security clearance revoked by Australia's domestic spy agency in 2011.

The agricultural trade specialist was accused of having unreported contact with foreign spies while working as a section manager in the Agricultural Trade Section at the Department of Agriculture, Fisheries and Forestry.

The Australian Security Intelligence Organisation claimed Dr Kim of being involved in “foreign interference" with South Korea's National Intelligence Service.

ASIO alleged Dr Kim had passed information to an NIS operative about negotiations over a bilateral trade agreement between Canberra and Seoul.

Dr Kim challenged the adverse security assessment in the Administrative Appeals Tribunal and then the Federal Court.

But much of the information, evidence and submission relevant to the case was suppressed – even from Dr Kim and his legal team – after the Attorney-General issued two security certificates.

Dr Kim asked the Federal Court to set aside the certificates and release the material, arguing the lack of access was a denial of natural justice and procedural fairness.

But Justice Lindsay Foster earlier this month threw out the request, saying Dr Kim's challenge had come too late.

The judge said the certificates should have been challenged when they were issued, which was months before the tribunal hearing.

“He did not do so prior to that time. His failure to do so led to the inevitable consequence that the hearing before the AAT was conducted, as required by law, upon the basis that the certificates had to be respected,” Justice Foster wrote.

“In my judgment, it is now too late for the applicant to attack the certificates.

“He cannot stand by and watch while the certificates are deployed against him and then subsequently seek to challenge them when it becomes apparent that they were a significant contributor to the applicant’s loss in the AAT.”

Justice Foster said to find otherwise would undermine the integrity of the tribunal’s procedures.

Dr Kim's full challenge will be heard in November.