For everything we know about the Ben Zygier spy scandal, there are a dozen things we don't.

Even after this week's Department of Foreign Affairs and Trade report, we still know a fraction of the full story.

It's likely to stay that way.

The DFAT report poses more questions than it answers but the Gillard government has made it clear it doesn't intend to dig any deeper.

Israel is still investigating the case, but given the extraordinary lengths they've gone to so far to cover it up - and shield its spy agency Mossad from any fallout - it's unlikely we'll ever get the whole, unvarnished truth.

So what do we know?

Ben Zygier was born in Australia in 1976. He trained as a lawyer in Melbourne and was by all accounts a likeable guy. In 2000 he moved to Israel, took out dual citizenship and married an Israeli woman. They had two children.

Releasing the DFAT report on Wednesday, Foreign Minister Bob Carr confirmed for the first time that Zygier worked for the Israeli government. He stopped short of confirming Zygier was a Mossad spy, but certainly indicated he was.

"You can draw your own conclusions," he said.

When was he recruited? We don't know. But in 2010 something went horribly wrong with his espionage career.

Israeli authorities arrested Zygier on January 31 for as yet undisclosed national security offences and jailed him in a maximum-security cell specifically designed to hold the assassin of Israeli Prime Minister Yitzhak Rabin.

What is he actually accused of doing? We have no idea. But it must have been serious: the DFAT report reveals he was facing up to 20 years' jail.

Israel dubbed him "Prisoner X" and imposed a strict gag order on local media, effectively banning them from writing anything about it. It's fair to say Zygier was one of the nation's most sensitive secrets, although it should be noted his lawyer and family were given permission to visit him on dozens of occasions.

After about 11 months in his supposedly suicide-proof cell, Zygier died. The cause of death was listed as "asphyxia by hanging".

How did this happen when he was supposed to be under constant supervision?

Again, no answer's been given.

It was only after Zygier's death, in mid-December 2010, that Australia's ambassador to Tel Aviv found out he'd even been incarcerated.

The embassy helped arrange for his body to be returned to Melbourne, where he is buried in a Jewish cemetery.

But other Australian officials knew about Zygier's arrest much earlier. Israel told ASIO spooks on February 16, about two weeks after his arrest. Eight days later, ASIO briefed senior DFAT officials Dennis Richardson and Greg Moriarty.

This briefing occurred the very same day Dubai authorities told the Rudd government that Mossad agents had used Australian passports to enter the UAE to assassinate Hamas leader Mahmoud al-Mabhouh.

Richardson and Moriarty are two of Australia's most capable and well-respected public servants: Richardson is a former ASIO boss, ambassador to the US and now head of the Defence department; Moriarty is ambassador to Indonesia.

What happened after the briefing is a little murky.

Moriarty says he briefed then-foreign minister Stephen Smith's chief-of-staff Frances Adamson on the case. But Adamson - now ambassador to China and also very well-regarded - told the DFAT review she could not remember any such conversation.

Smith says he has no recollection of ever being briefed by Adamson or anyone else.

ASIO briefed his office twice more - in March and May 2010 - but still Smith says he has no recollection of ever being told.

The DFAT report notes there is no evidence he was personally briefed. But surely he should have been.

Did his staff not think it important? Did they intentionally shield him from the news?

Then-prime minister Kevin Rudd also says he doesn't remember ever being told about the case, even though one of his closest confidantes - foreign policy adviser and later chief-of-staff Philip Green - was apparently briefed.

Rudd says he wasn't even told about the case when he visited Israel as foreign minister in December 2010, just days before Zygier's death.

Then-attorney general Robert McClelland admits he was told. He says ASIO briefed him shortly after the arrest and he's confident the agency did nothing wrong. He's the one that authorised ASIO to brief Smith and Rudd's offices.

But that appears to be where he left it.

McClelland, like everyone else who knew about Zygier's arrest, decided it was an intelligence case - not a consular matter - and left it in ASIO's hands.

And that's a key criticism in the DFAT report. It acknowledges that its officials should have done more.

Most notably, it should have told the Tel Aviv embassy about Zygier's arrest so the ambassador could have offered consular support - although it's reasonable to assume the Israelis would have blocked access - and followed-up on Israel's assurances he was being treated properly.

The same day that Carr released the DFAT report, the Inspector General of Intelligence Services - essentially Australia's spy watchdog - unexpectedly revealed it had conducted a brief review of ASIO's handling of the case.

"I have come to the conclusion that there is no evidence that ASIO has acted improperly or unlawfully in this matter," Inspector-General Vivienne Thom said, adding there was no need for a more comprehensive inquiry.

Details were scant. Dr Thom appeared to expect his conclusions would be accepted at face value.

Current Attorney-General Mark Dreyfus says he doesn't see the need for any further probes either.

There are other pressing questions too.

Does Zygier's case relate in anyway to Israel's misuse of Australian passports?

What is known is that during the ten years he lived in Israel, Zygier had three different Australian passports in three different names - Ben Zygier, Ben Burrows and Ben Allen.

Australia was quite rightly outraged by the news from Dubai and expelled an Israeli diplomat from the country in retaliation. How is it that none of the very intelligent people who knew about Zygier's arrest link him to the passports issue?

Was Zygier involved in the Dubai hit in anyway? Carr says there's no evidence to suggest he was, but we don't know for sure.

Did Zygier use his Australian passports for other Mossad operations to get into countries from which Israelis are banned?

Why else would he need three different passports in three different names?

Carr has warned Israel that if any further passport abuse is confirmed, Australia won't take it lightly.

"If the world thinks that Australian passports are routinely debauched by another country then Australians presenting their passports all over the world could well place their lives in danger. We can't live with that," he said.

But has he or anyone else in the government actually sought any assurances from Israel on this?

On Wednesday Carr said only that he "reserves the right" to seek more information from the Israeli government.

And a final important question, in light of reports that Zygier was one of three dual Australian-Israelis recruited by Mossad.

Where are the other two?