Attorney-General Christian Porter says the case of Canberra's secret prisoner is "unique" to his knowledge.
Mr Porter has shared new details of the case of the man known as Alan Johns.
The former military intelligence officer was jailed for two years and five months after pleading guilty to five charges related to the mishandling of classified information. He was released earlier this year on the proviso of good behaviour for three years.
His trial, sentencing and prison sentence was carried out in secret. The case only came to light when Mr Johns took action against the prison in the ACT Supreme Court arguing an abuse of power after correctional officers tipped police off to a memoir he was writing.
In a response to questions on notice from Centre Alliance Senator Rex Patrick, Mr Porter said he approved the prosecution of Mr Johns, after he communicated confidential information "contrary to a lawful obligation not to do so".
"The information was of a kind that could endanger the lives or safety of others. This risk remains," Mr Porter said.
The National Security Information Act was invoked to stop any sensitive details emerging from legal proceedings.
"The court made orders under section 22 of the National Security Information Act, with the consent of the parties, protecting the national security information," Mr Porter said.
"The orders provided for a mechanism for closure of the court in circumstances where highly sensitive national security information would have been disclosed, but did not prevent the defendant or his counsel from accessing the information."
Mr Porter also said the Supreme Court orders allowed Mr Johns to reveal his conviction involved the mishandling of classified information.
"The orders did provide for the defendant to inform persons that the disclosure of the nature of his offending or the provisions against which the defendant was charged and convicted is prohibited by order of a court, and that further inquiries may be directed to the Attorney-General's Department," Mr Porter said.
Mr Porter said the laws balanced the need to protect national security with the principle of open justice.
"The nature of the national security information involved in this proceeding informed the Commonwealth's position to seek protective orders," Mr Porter said.
"The matter is unique in my experience, and I am not aware of any other similar cases."
But Senator Patrick said the Attorney-General had failed to answer key questions about the case.
"Mr Porter's response falls woefully short of what his position as the first law officer of the Commonwealth, responsible to the Parliament, requires," Senator Patrick said.
"The Attorney-General has declined to reveal the actual charges brought against 'Alan Johns'. We still don't know what national secrecy law underpinned the charges. We still don't know which intelligence agency was involved.
"The Attorney-General notes that these matters are subject to court orders imposing secrecy, but he is the responsible authority that sent his representatives into the courts to argue for a total information blackout."
Because of the secrecy, Senator Patrick argued there was no accountability for the agency involved.
"This is significant because it is claimed by 'Alan Johns' that a failure by his agency to respond to significant mental health issues was part of the circumstances that led to him being charged," Senator Patrick said.
"The 'Alan Johns case' raises very serious concerns about the extent to which national secrecy laws have encroached on and compromised the vital principle of open justice in Australia. In this instance we have had secret charges laid, a secret trial, a secret conviction, a secret sentencing and a secret imprisonment. The total secrecy imposed on this matter must not be a precedent for future."
The case has previously drawn concerns from the legal profession and also within the Australian parliament.
Retired ACT Supreme Court judge Richard Refshauge said the secrecy was "bewildering".
Greens senator Nick McKim said it proved Australia needed a charter of rights.
"What we know now is in the 21st century there is a person secretly charged, secretly sentenced and secretly imprisoned in Australia," Senator McKim said.
"This is a shocking example of secrecy and abuse of state power and our descent into a police state and yet another argument for a charter of rights in Australia."