Shane Rattenbury says he too was kept in the dark about the prisoner's existence, who was prosecuted and jailed in the capital for charges unknown to the public or the jail.

Meanwhile, retired ACT justice Richard Refshauge told The Canberra Times the extraordinary circumstances of the case were crying out for explanation.

The prisoner, given the alias "Alan Johns" by the government, was prosecuted and convicted while hidden from the public.

Not even prison bosses were privy to the man's true identity or the nature of the charges that had put him in jail.

"I am deeply disturbed by the extraordinary levels of secrecy surrounding the 'Witness J' case: secrecy that is a direct result of the Commonwealth government's apparent growing disregard for the principles of open justice and a robust democracy," Mr Rattenbury said.

"It is disturbing that Canberrans, along with other Australians, only learned about this case after the fact due to the restrictive Commonwealth legislation.

"I include myself in this group - despite my role as minister in a territory government, I was not advised in relation to this issue," he said.

The minister said the ACT justice system operated in accordance with the relevant legislation.

"The case, including matters relating to non-disclosure of identity and details, were governed by Commonwealth law and applied to specific facts by a fully independent member of the judiciary."

Retired ACT Supreme Court judge Refshauge said that from time to time there was a need for secrecy in the courts.

"But that need has to be moderated by an overwhelming obligation for the courts to do their business in public, so that they can be transparent and accountable," he said.

"I find it bewildering that there is so much secrecy about this and the need for it is unexplained, which is depressing.

"The need for transparency and accountability of the courts is so fundamental to the confidence of the community in our system ... such an extraordinary circumstance cries out for explanation."

The secret prisoner, understood to be a former military intelligence officer, served time in the Alexander Maconochie Centre from 2018 until August this year.

A set of Commonwealth orders - the details of which were secret to both the prisoner and the prison - barred sharing of information about his offending or identity.

He was also restricted in his communications with family and friends while serving his sentence. Federal police had asked the prison to let it know if any unusual visitors tried to see him.

Meanwhile, under a mental health plan developed with his treating nurse, the inmate began writing a memoir of his time in prison.

He sent a copy of the memoir to his brother, who got in touch with Canberra author Robert Macklin.

But when Mr Macklin booked in to see the prisoner, his visit was refused, with police concerned about a visit from the author.

Federal police officers raided the prisoner's cell, the prison servers and his brother's house.

The prison restricted the use of his emails.

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The existence of his case only came to light when the prisoner took civil action against the jail for telling police about the memoir and the withdrawal of his email privileges.

A judgement rejecting the man's case against the jail was published but contained no detail about the offending or his identity. The man was ordered to pay costs but the ACT government said it had not yet considered the matter of pursuing those costs.

Barrister Ken Archer, who is one of a group of lawyers representing Bernard Collaery, the lawyer being prosecuted under Commonwealth secrecy provisions over the exposure of an Australian bugging operation in East Timor, said the whole case was absolutely alarming.

"What public interest is served by the person being incarcerated for reasons that are not known to anybody?" he said.

The whole foundation of the criminal justice system is predicated on the assumption that cases are open to the public, and justice is not only done but seen to be done, he said.

"Secrecy of this type - which as far as we know is completely unprecedented - is not consistent with the criminal justice process as we know it. It is very frightening."

Mr Archer said there was no way for anyone to know the merits of the case.

"We don't know how or why a court was persuaded that was an appropriate course," he said.

"We do not know how the person could be appropriately accommodated in prison if the AMC knows little or nothing about the prisoner or his case."