Australian officials knew about the detention of Melbourne man and suspected Israeli spy Ben Zygier shortly after his 2010 arrest, but it's unclear whether they told then-foreign minister Stephen Smith.

Department of Foreign Affairs and Trade head Peter Varghese has given Foreign Minister Bob Carr an interim report detailing who knew what about the mysterious case that has rocked the Australian and Israeli governments.

The report confirms Australian intelligence agencies had told DFAT officials about Mr Zygier's detention in a maximum security prison for alleged offences under Israeli national security laws shortly after his arrest in February 2010.

Senator Carr - who ordered a review of the case after receiving conflicting advice about who knew what and when - says Australian officials sought assurances his legal rights would be respected, that he had legal representation, that his family had been informed, and that he was not being mistreated.

"The Israeli government further advised the Australian government that the individual would be treated in accordance with his lawful rights as an Israeli citizen," Senator Carr told a Senate estimates hearing in Canberra on Thursday.

"The Australian government relied on these assurances."

At no stage did the Australian government receive any request for consular support from Mr Zygier - a dual Australian-Israeli citizen also known as Ben Allen and Ben Alon - or his family, Senator Carr said.

Mr Varghese said the matter was dealt with through "intelligence channels" and Australia's embassy in Tel Aviv wasn't made aware of the case until Mr Zygier died, apparently by his own hand, on December 15, 2010.

He hadn't yet been able to find out whether DFAT briefed Mr Smith about the case.

"I haven't yet been able to establish if the then-foreign minister in February 2010 had been briefed by the department," Mr Varghese said.

He hoped to deliver a more comprehensive report on the matter by the end of next week.

While the circumstances surrounding Mr Zygier's detention are unclear, it's believed he worked for Israeli spy agency Mossad.

Israel on Thursday admitted for the first time it had held a man with dual citizenship under a false name for security reasons. Israeli media reports have suggested he was detained for treason.

A judicial inquiry recently ruled he took his own life, Israel's Justice Ministry said in a statement.

It is believed Mr Zygier was the mysterious figure known as Prisoner X and was until this week one of Israel's most sensitive national security secrets.

In May 2010 Israel's Ynet news website ran a story titled "Who are you, Mr X?", about a prisoner being held in top-secret conditions whose identity and crime weren't even known to his jailers. The story was quickly taken offline under a strict gag order.

The ABC's Foreign Correspondent program revealed the Australian connections this week.

Mr Zygier was a lawyer who moved from Melbourne to Israel in 2000, married an Israeli woman and fathered two children.

Seven days after he was found hanged in his cell at age 34, his body was flown to Melbourne, where he was buried in a Jewish cemetery.

Australian Greens leader Christine Milne said it was clear the Australian embassy in Tel Aviv had been sidelined.

"The question is why was the fate of an Australian citizen left to be determined by ASIO and ASIS?" she said.


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