Mr Collaery did not attend court on Wednesday as procedural elements of his case were worked out by lawyers appearing predominantly over video link.

Former attorney-general Christian Porter gave the green light for prosecution to start in 2018, with Mr Collaery accused of unlawfully sharing classified information about the alleged bugging operation of the East Timor prime minister by Australian officials in 2004.

Current Attorney-General Michaelia Cash has continued the prosecution and appealed to the High Court to keep a judge's ruling secret.

The judgment from ACT Chief Justice Helen Murrell which the Commonwealth is trying to stop being published in full derided the prosecution for seeking to have a trial conducted in secret.

An initial push to not have the judgment published was refused.

Chief Justice Murrell ruled closing the case to the public would damage confidence in the justice system with open courts standing as a bulwark against possible political prosecutions.

Her judgment on the ruling has not yet been published in full with the Attorney-General's Department arguing the information in the judgment is likely to prejudice national security.

In its High Court submission, first obtained by the Human Rights Law Centre, the attorney-general argues classified information in the judgment would be made public.

HRLC senior lawyer Kieran Pender pointed to the irony of trying to keep a judgment advocating for an open court behind closed doors.

"Rather than appealing the secrecy of a judgment that said no to secrecy to the High Court, the Attorney-General should drop the prosecution and fix our broken whistleblower laws," he said.

"Whistleblowers should be protected, not punished, and certainly not dragged through an endless, opaque prosecution.

"Changes to Australia's whistleblowing laws are long overdue and that reform, rather than the prosecution of whistleblowers, should be the Attorney-General's priority."

Australian Associated Press