Israel has confirmed the reported suicide of an Australian prisoner who had worked for the Israeli spy agency Mossad.

Israel broke its silence on Wednesday after Australia's ABC news network first revealed the identity of Prisoner X, a 34-year-old man who had used three different names, including Ben Zygier, Ben Allen, and Ben Alon.

After initially denying that he knew nothing about the case, Australia's Foreign Minister Bob Carr said on Thursday that his government did know that an Australian was detained by Israel in February 2010 for national security offences.

On Wednesday, he said Australian diplomats in Israel only knew about Zygier's detention after his death in custody later that year.

Carr told an oversight committee of Australian legislators that Canberra was told about Zygier's detention on February 24, 2010, just after his arrest over "serious offences under Israeli national security legislation".

Foreign ministry secretary Peter Varghese said the information was not given to Australian diplomats but "came in another form, from another channel". He gave few other details.

After appeals by Israeli media chafing at censorship of a story broken by ABC, a district court near Tel Aviv allowed publication of six paragraphs of sanctioned text - a de facto preliminary account by the state.

The text said an Israeli with an unspecified dual nationality had been secretly imprisoned "out of security considerations", only to be found hung in his cell two years ago in what was eventually ruled a suicide.

The district court did not confirm or deny ABC's unsourced findings that the dead man was 34-year-old Ben Zygier, an Australian who moved to Israel and may have been jailed in isolation over suspected misconduct while spying for Mossad.

Social media records showed that Zygier, who came from a prominent Jewish family in Australia and was buried in Melbourne, had been married with children. His relatives have declined all comment on the case.

Former friends in Australia said Zygier had been a lawyer and used to recount stories of his time in the Israeli military.

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Aljazeera