Sydney: Most details relating to Indian doctor Muhammad Haneef's incarceration on terror charge and subsequent release will remain an enigma as the judge heading the judicial inquiry into his case has declared that much of the information he has cannot be made public.

In a message posted Monday on the inquiry website, former New South Wales Supreme Court judge John Clarke, who is heading the judicial inquiry, said: "Since I was appointed to conduct this Inquiry in March 2008, I have endeavored to meet the desire of the Attorney General and my own assurances to make public as much of the proceedings and material before the Inquiry as was possible without jeopardising matters of national security or pending trials in Australia or overseas."

"Reluctantly, I have today advised the Attorney General (Robert McClelland) that it will not be feasible to make public as much information as was initially envisaged."

The Clarke inquiry is investigating the series of events from the arrest of Haneef at Brisbane airport July 2, 2007, until his release from detention and return home to Bangalore July 29.

Haneef was incarcerated after being charged with supporting a terrorist organisation by "recklessly" giving his mobile phone SIM card to people planning the botched London and Glasgow bomb attacks. The charges were later dropped and Haneef returned to his family.

His work visa was reinstated last December by new Immigration Minister Chris Evans.

Justice Clarke said he had been given a vast amount of relevant material by the commonwealth and state departments and agencies and also by Haneef's representatives.

"A very high proportion, however, of the material from departments and agencies carries a security classification which limits the extent to which it can be shown to other people or disclosed generally," Justice Clarke said.

He had not sought the declassification of the documents because he said the hurdles would be "virtually insurmountable".

The originating agency alone had the authority to remove the classification and the inquiry had not been given authority to publish classified material, the judge said.

A spokesman for the attorney general told Australian Associated Press (AAP): "The government accepts Clarke's decision as sensible approach to progressing the inquiry's important work in fully examining the facts of the Haneef matter and reporting to government."

Haneef's lawyer Peter Russo said Justice Clarke's move would continue to shroud in secrecy the roles of the Australian Federal Police (AFP) and the federal Director of Public Prosecutions (DPP) office.

"It was an important process that needed to be gone through for the Australian public to have any degree of confidence that the AFP know what they're doing. It was their opportunity to come clean and they've obviously elected not to do that," Russo told AAP.