Revelations about a man being tried and imprisoned in secrecy, and the fluke discovery of the case, have revived calls for Australia's secrecy laws to be reviewed.

Exactly how the case of "Witness J" came about remains a mystery.

It's left some wondering how it can occur in a society founded on the principle of open justice.

The nation's chief law officer insists secrecy was needed to protect national security.

"The court determined, consistent with the Government submission, that it was contrary to the public interest that the information be disclosed and the information was of a kind that could endanger the lives or safety of others," Attorney-General Christian Porter told the ABC.

While suppression may be used in family or child-related matters to reduce harm to individuals, the danger posed by information deemed a threat to national security is less direct.

This is how a national security trial can become so secret that the public doesn't even know it exists ... and why.

What exactly does a secret trial look like?

Law Council president Arthur Moses says secret trials occur in ordinary courtrooms where evidence can be recorded and where there are security facilities for people in custody.

"However, the door to the courtroom will be closed and generally locked, with a sign saying 'closed court'," he says.

"The details of the case will not be found on the court website, or on the noticeboard with the list of all the other cases."

Although he has some knowledge of secret trials, Mr Moses is not aware of how many completely secret trials — where there is no indication even of the trial's existence — have occurred.

The fate of Witness J has been decided inside closed Canberra courtrooms. ( ABC News: Ian Cutmore )

And he can't be sure exactly how they come about, given various secrecy provisions exist.

"That leaves both the profession, and indeed the media, in the position that it's operating in a vacuum."

Laws that let courts work in secret could come from the Commonwealth Criminal Code, the common law, state laws or the National Security Information (Criminal and Civic Proceedings) Act, also known as the NSI Act.

A 15-month inquiry by the Australian Law Reform Commission in 2010 identified 506 secrecy provisions in 176 pieces of Commonwealth legislation, including 358 criminal secrecy offences.

How they might happen

One case which might shed light on how secret trials work is that of Witness K, in which an ex-spy pleaded guilty to breaching the Intelligence Services Act in relation to allegations that Australia bugged East Timor's cabinet room during sensitive negotiations between the two countries. The matter is still ongoing.

Heavy secrecy orders have applied to the case, drawing the interest of Ernst Willheim, a visiting fellow at ANU and a former government legal advisor.

In a submission to the Witness K case, he looked at how courts should take national security considerations into account.

In that case, he says it "appeared" the Attorney-General issued a non-disclosure certificate under the NSI Act, which can prevent the defendant from disclosing sensitive information.

In 2008, Labor's then-attorney-general Robert McClelland issued a step-by-step guide for how to manage national secrecy information under the NSI Act.

For a non-disclosure certificate to be issued, the Attorney-General must:

Expect that a party or witness will disclose information, and

Expect that a party or witness will disclose information, and Consider that disclosure of the information would be likely to prejudice national security.

The court considers this alongside arguments for keeping a trial open, before it decides whether — and to what extent — secrecy will be applied.

Arthur Moses SC wants more information released about secret trials. ( Supplied: New Chambers )

Mr Moses says someone arguing to keep a trial open might not be able to obtain the arguments for making it closed, and therefore be unable to address them directly.

"That has happened and may happen — and then those acting for the accused, all they really can do is provide the court with assistance in relation to the general principles."

One option is seeking to get both parties to agree on secrecy.

In response to questions relating to Witness J last week, Senator Marise Payne told the Senate on behalf of Mr Porter, who sits in the House of Representatives, that "there are court orders in place restricting the disclosure of the information in this matter".

"Those orders were made with the consent of the parties," she said.

Until Thursday's revelations, this was perhaps the most that had been revealed about the case.

But the existence of the agreement only came to light long after the trial, and opportunities for debate have passed.

And the orders aren't public, so their terms and the nature of the consent are impossible to verify.

Getting the balance right

Mr Willheim argues open justice is a "fundamental principle".

"Confidence in the administration of justice is diminished if trials are in secret," he says.

Centre Alliance senator Rex Patrick has argued that completely secret trials should never be held, except at times of war, while the Law Council has called for a review of secrecy laws.

Attorney-General Christian Porter has responded to concern over the level of secrecy applied to Witness J's trial. ( ABC News: Matt Roberts )

A spokesperson for Attorney-General Christian Porter says the Government has asked the Parliamentary Joint Committee on Intelligence and Security to conduct an inquiry into how law enforcement and intelligence powers impact on freedom of the press.

"This inquiry has received submissions on a range of matters, including submissions on the operation of secrecy offences," the spokesperson told the ABC.

"The Attorney-General's view is that as far as it is possible, legal proceedings should be conducted in open court."

Mr Moses also argues there should be no secret trials, and the nature of the offence and the provision under which the defendant was charged should be released.

"At the end of the day, justice is administrated in the name of the people, so basic information should be provided in order to enable the public to know why this has occurred," he says.

"It also enables bodies such as the Law Council to explain the issues to the public in order for the public confidence in the administration of justice being maintained."

The Parliamentary Joint Committee on Intelligence and Security is due to hand down its report on December 16.