Like the fictional Man in the Iron Mask, Israel's infamous "Prisoner X" was allegedly held in solitary confinement in conditions of such strict secrecy that even his own jailers were told neither his name nor the crime he had allegedly committed.

The man's identity became the subject of intense speculation when he was reportedly found hanged in his cell in 2010, but the prisoner's existence has never been officially acknowledged by Israel's government, which has gone to extraordinary lengths to stifle media coverage of the case. Now, however, new evidence has been uncovered by the Australian Broadcasting Corporation that strongly suggests Prisoner X was an Australian citizen, Ben Zygier, whom it described a Mossad agent.

Although there has been no intimation of the accusations against Zygier, commentators have suggested it could only suggest the most serious kind of security case, perhaps involving treason.

In the immediate aftermath of ABC's claims, the Israeli newspaper Haaretz reported that the Israeli prime minister's office had called "an emergency meeting of the Editors Committee … to ask its members to co-operate with the government and withhold publication of information pertaining to an incident that is very embarrassing to a certain government agency".

Later in the day the gagging orders were explicitly linked to the claims about the dead Australian by several Israeli MPs who also raised questions about the affair during a debate in the Knesset.

Asked by an Arab MP about "reports [of the suicide of] an Australian citizen who was in Israeli custody under a different identity", the justice minister, Yaakov Ne'eman, replied: "I cannot answer these questions because the matter does not fall under the authority of the justice minister. But there is no doubt that if true, the matter must be looked into."

A second MP, Dov Henin, asked: "Are there people in prisons whose incarceration is kept secret? What are the supervision mechanisms on this kind of imprisonment? What are the possibilities for parliamentary supervision on such incarcerations? How can the public be critical in this situation?"

A new documentary screened this week for ABC's Foreign Correspondent programme claims Zygier used the name Ben Alon or Ben Allen after moving to Israel. He was secretly imprisoned in Ayalon prison in Ramla in the wing built to accommodate Yigal Amir, the assassin of the Israeli prime minister Yitzhak Rabin, ABC reported.

The 34-year-old was married to an Israeli woman and was the father of two young children. He had reportedly spent a number of months in the cell before his death.

Zygier's father Geoffrey, a prominent leader of the Melbourne Jewish community, apparently refused to speak to the programme makers.

The only comparable case that has come to light was Israel's secret imprisonment for more than 10 years of the KGB spy Marcus Klingberg after he was tried under a false identity.

Australia's department of foreign affairs and trade (Dfat) on Wednesday launched a review into how its diplomats handled the case.

The review, to be conducted by the department's secretary, Peter Varghese, was announced after it became known that certain department officers had been made aware in 2010 that Zygier was being held in jail in Israel but did not pass the information on. "Dfat had [originally] advised that it was unaware of Mr Allen's detention in Israel," a department spokesman said. "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."

Earlier the foreign minister, Bob Carr, had said consul officials were not aware of the man's circumstances until his parents asked for help in bringing his body back to Australia. Under normal circumstances foreign embassies are advised if one of their nationals is being held in prison.

The case of Prisoner X first came to international attention in a flurry of stories in 2010. Coverage talked about the existence of an unidentified man being held in conditions of absolute secrecy for an undisclosed crime, which prompted a media guessing-game over his identity, with some speculating he was an Iranian general.

According to accounts at the time, even his guards were not aware of the prisoner's identity or the crime he had allegedly committed.

Debate over the existence of Prisoner X was shortlived, however, with the story disappearing from the Haaretz website.

Speculation that the Israeli government had imposed a media blackout prompted Dan Yakir, the chief legal counsel with the Association for Civil Rights in Israel, to write to the country's attorney general and demand that the "blackout be eliminated".

On Monday Haaretz printed a heavily pixellated image of what it said was the original document enforcing a reporting ban.

The existence of the blackout appeared to be confirmed by the call for a reporting ban in the immediate aftermath of the Australian report.

According to ABC, circumstantial evidence for its identification of Zygier was provided by the repatriation of his body to Melbourne from Tel Aviv a week after Prisoner X was allegedly found hanged in his cell.

The programme claimed that Zygier had a second passport in the name of Ben Allen at the time of the repatriation of his body.

Commenting on ABC's disclosures, the Australian foreign minister, Bob Carr, said he was concerned by the claims. "Those allegations certainly do trouble me," he said.

"It's never been raised with me. I'm not reluctant to seek an explanation from the Israeli government about what happened to Mr Allen and about what their view of it is. The difficulty is I'm advised we've had no contact with his family [and] there's been no request for consular assistance during the period it's alleged he was in prison.

"Even if Prisoner X has now been identified, his crime remains a mystery although it has been widely speculated that it would have involved treachery to warrant such extreme measures."

Details of one of two gagging orders acquired by the Israeli government have been disclosed to the Guardian .

Israel first sought to prevent reporting of the case in an injunction it sought in March 2010. A second "clarifying order" was issued by Judge Hila Gerstel of the central district court, making clear that the reporting ban referred to all Israeli media and preventing any discussion of the man who had been referred to variously as "Prisoner X", "Mr X" or "cell 15 in Ayalon prison".

The court's involvement on two different occasions suggests some kind of judicial oversight of the case, but neither the man's identity nor the charges he was facing were made clear.

Bill van Esveld, a researcher for Human Rights Watch, said the case raised serious questions about fundamental prisoners' rights including lack of due process, what information was given to the man's family and rights of consular access under international treaty obligations.

"We only know the absolute bare bones of this case. We know that there was some kind of gagging order and it would be almost unheard of to involve a judge to silence a story that had no basis in truth.

"The main concern is over the fact that a person cannot simply be disappeared. That is against the norms of international law. That person's family needs to know what has happened to them. They have to be able to have access to a defence attorney and their government needs to be informed to permit consular access."