Evidence has been unearthed that strongly suggests Israel's infamous Prisoner X, who was jailed under extraordinary circumstances in 2010, was an Australian national from Melbourne.

Investigations by the ABC's Foreign Correspondent program have revealed Ben Zygier, who used the name Ben Alon in Israel, was found hanged in a high-security cell at a prison near Tel Aviv in late 2010.

His body was flown to Melbourne for burial a week later.

The death goes part of the way to explain the existence in Israel of a so-called Prisoner X, widely speculated in local and international media as an inmate whose presence has been acknowledged by neither the jail system nor the government.

The 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.

The Prisoner X cell is a jail within a jail at Ayalon Prison in the city of Ramla. It was built for the assassin of Israeli prime minister Yitzhak Rabin.

The ABC understands Mr Zygier became its occupant in early 2010. His incarceration was so secret that it is claimed not even guards knew his identity.

Israeli media at the time reported that this Prisoner X received no visitors and lived hermetically sealed from the outside world.

When an Israeli news website reported that the prisoner died in his cell in December 2010, Israeli authorities removed its web pages.

An Israeli court order prohibiting any publication or public discussion of the matter is still in force; Israel's internal security service, Shin Bet, has effectively blocked any coverage of the matter.

Secret imprisonment

Foreign Correspondent can reveal that Mr Zygier was 34 at the time of his death and had moved to Israel about 10 years earlier. He was married to an Israeli woman and had two small children.

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

It is understood Mr Zygier "disappeared" in early 2010, spending several months in the Prisoner X cell.

At the time, human rights organisation Association for Civil Rights in Israel criticised the imprisonment and wrote to Israel's attorney-general.

"It's alarming that there's a prisoner being held incommunicado and we know nothing about him," wrote the association's chief legal counsel Dan Yakir.

The assistant to the attorney-general wrote back: "The current gag order is vital for preventing a serious breach of the state's security, so we cannot elaborate about this affair."

Contacted by the ABC, Mr Yakir would not comment on the case, quoting a court order gagging discussion.

Bill van Esveld, a Jerusalem-based advocate for Human Rights Watch, has described the secret imprisonment of Prisoner X as "inexcusable".

"It's called a disappearance, and a disappearance is not only a violation of that person's due process rights - that's a crime," he told Foreign Correspondent.

"Under international law, the people responsible for that kind of treatment actually need to be criminally prosecuted themselves."

Mr Zygier's apparent suicide in prison adds to the mystery. He was found hanged in a cell with state-of-the-art surveillance systems that are installed to prevent suicide. Guards reportedly tried unsuccessfully to revive him.

His body was retrieved and flown to Melbourne. He was buried in Chevra Kadisha Jewish cemetery in the suburb of Springvale on December 22, seven days after his death.

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

Mossad activity

Australia's domestic intelligence agency ASIO has long scrutinised Australian Jews suspected of working for Mossad.

The agency believes Mossad recruits change their names from European and Jewish names to "Anglo" names. They then take out new passports and travel to the Arab world and Iran, to destinations Israeli passport holders cannot venture.

Warren Reed, a former intelligence operative for Australia's overseas spy agency ASIS, told Foreign Correspondent that Australians were ideal recruits for Mossad.

"Australians abroad are generally seen to be fairly innocent," he said.

"It's a clean country - it has a good image like New Zealand.

"There aren't many countries like that, so our nationality and anything connected with it can be very useful in intelligence work."

The Department of Foreign Affairs has confirmed that Mr Zygier also carried an Australian passport bearing the name Ben Allen.

'Allegations troubling'

When told details of Foreign Correspondent's investigation, Foreign Minister Bob Carr said he was concerned by the claims.

"Those allegations certainly do trouble me," Senator Carr 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."

Senator Carr says in the absence of a complaint by Mr Zygier's family, there is little for the Australian Government to act upon.

International conventions spell out that when a foreigner is jailed or dies, their diplomatic mission must be informed.

Senator Carr claims Australian diplomats in Israel only knew of Mr Zygier's incarceration after his death.

Mr van Esveld says it is inexcusable for the Australian Government not to be notified.

"The obligation of one country to notify another when the other citizen has been arrested, detained, especially if they die - that is so basic. It is called customary law," he said.

"Which means that even if Israel didn't ratify a treaty saying it has to notify the other country, it still has to do so because that is such a basic norm of interstate relations."

The greater mystery is why Mr Zygier was imprisoned under such secrecy.

Sources with connections to Israel's intelligence community have told Foreign Correspondent his predicament would have been "extreme" to warrant such harsh treatment.

Former ASIS operative Mr Reed told the ABC: "However the transgression came about, it would have to be involved with espionage, treachery - very, very sensitive information that known to others would pose an immediate threat to Israel as a nation state."