Foreign Affairs Minister Bob Carr has confirmed his department was made aware in 2010 that an Australian man, believed to be Prisoner X, was being held in a super-secret Israeli jail.

The ABC's Foreign Correspondent program revealed on Tuesday the likely identity of Prisoner X as Melbourne man Ben Zygier - aka Ben Alon or Ben Allen - who was found dead in a prison near Tel Aviv in late 2010.

A spokeswoman for Senator Carr says the Minister was initially advised that the Department of Foreign Affairs (DFAT) was unaware of Mr Zygier's detention.

"DFAT has now advised that some officers of the department were made aware of Mr Allen's detention at the time in 2010 by another Australian agency," the spokeswoman said in a statement.

"Minister Carr has asked department secretary, Mr Peter Varghese, to review the handling of this consular case."

Mr Zygier's arrest and jailing in Israel remains a mystery, but the ABC understands he had been recruited by spy agency Mossad.

It is understood he "disappeared" in early 2010, spending several months in the Prisoner X cell at Ayalon Prison in the city of Ramla before being found dead.

Censorship lifted

The Prisoner X case is regarded as one of the most sensitive secrets of Israel's intelligence community, with the government going to extraordinary lengths to stifle media coverage and gag attempts by human rights organisations to expose the situation.

But Israeli MPs and commentators are now asking tough questions about the mysterious detention and apparent suicide of Prisoner X, following the ABC's report.

Twenty-four hours after Foreign Correspondent broke the story, the Israeli censor moved to ease the total blackout on coverage of the incident, allowing the local press to publish details from the report.

On Tuesday Israeli media reported that prime minister Benjamin Netanyahu had called an urgent meeting with the country's top editors to ask them to cooperate by "withholding publication of information pertaining to an incident that is very embarrassing to a certain government agency," Haaretz newspaper said, in a clear allusion to Mossad.

But shortly afterwards, three MPs raised questions over the issue in parliament, effectively sidestepping the censor in a move which forced a slight easing of the reporting restrictions.

Although the Israeli press can now quote foreign media on details of the case, the restrictions bar any original reporting on the incident, a spokesman for the censor's office said.

"It is now possible to report what foreign sources are saying about this story," a spokesman told AFP, saying the main blackout was still in place.

"It is based on a court order from 2010 and covers anything which could indicate the reason for his arrest."

Further questions are expected to be raised in Israel's parliament on Wednesday (local time) with outgoing internal security minister Yitzhak Aharonovitch likely to be in the spotlight.

But former foreign minister Avigdor Lieberman attacked the MPs for using their parliamentary immunity to get around the censor.

"Once again, certain MPs don't hesitate to identify with the enemy and take advantage of their parliamentary immunity to violate censorship," he said in an interview on Israel's army radio.

Sorry, this video has expired Foreign Correspondent reports on the Prisoner X case

Seeking explanation

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Listen Duration: 4 minutes 48 seconds 4 m 48 s DFAT admits it knew about Zygier's detention Download 2.2 MB

Israel'sembassy in Canberra has declined to comment, although its ambassador met Opposition foreign affairs spokeswoman Julie Bishop for a pre-arranged meeting on Wednesday.

Speaking before the meeting, Ms Bishop said she would be raising the case with the ambassador and was concerned the Israeli government was censoring media reports.

"That's a matter that I'll raise directly with the Israeli embassy to get an understanding of the basis for it," she said.

"If there are security considerations I can understand it, but if it's just about embarrassing a government agency, then that certainly requires an explanation and I'll be seeking one."

A spokesman for Ms Bishop says the ambassador undertook to pass on her concerns to "relevant authorities" in Israel.

Mr Zygier's musician uncle Willy Zygier, who is the partner of Melbourne singer Deborah Conway, told ABC Local Radio in Melbourne that he had "no idea what is true, what isn't true".

"All I know is there's a family tragedy. Every suicide is a tragedy. That's all I've got to say," he said.

Mr Zygier's family has previously declined to speak to the ABC, and friends and acquaintances approached by Foreign Correspondent in Melbourne had also refused to comment.

ABC/wires