SYDNEY – There is at least one other Prisoner X secretly held in an Israeli prison, according to the Australian author of a new book on Ben Zygier, the Melbourne-born Mossad agent who committed suicide in a maximum-security cell in 2010.

Rafael Epstein, who spent most of last year researching and writing “Prisoner X,” concludes that Zygier was “almost certainly” not Israel’s sole secret prisoner.

His contention comes despite a denial last year by Public Security Minister Yitzhak Aharonovitch soon after Prisoner X had been revealed as Zygier in an investigation by the Australian Broadcasting Corporation.

There are no anonymous prisoners in Israel, Aharonovitch said at the time, adding that the Israeli government “does not conduct itself in darkness.”

But Epstein retorts: “This is almost certainly not the case. I am shocked when the court documents relating to Ben’s case hint at another hidden prisoner in Cell 13 [at Ayalon Prison].”

He quotes MK Zahava Gal-On (Meretz), who responded to Aharonovitch. “In a democracy there can be no secret prisoners with no outside supervision of where and under what conditions they are being held. In a democracy ministers don’t lie to the Knesset or the public,” she said, adding that Aharonovitch’s denial was “befitting a totalitarian state.”

Epstein also cites Israeli civil rights lawyer Avigdor Feldman, who said of the second prisoner: “This affair points to far more severe failures than the ones committed by the defense establishment in Zygier’s case.”

According to Feldman, “We’re talking about secrets that if revealed will harm not only the security of the state, but primarily those organizations and their senior commanders who would lose their jobs.”

Epstein told Haaretz this week he wrote the book because the governments of Israel and Australia, as well as their respective spy agencies, have “simply hidden too much.”

Although he knew Zygier as a young Melbourne boy in the groups Netzer and Hashomer Hatzair, he said the wall of silence around the story was difficult to penetrate.

“It remains a mystery to me why the family did not call on the Jewish community’s considerable political connections in Canberra and Tel Aviv to argue their son’s case more forcefully,” he said.

The Zygier family received $1.2 million from the Israeli government “in exchange for agreeing not to pursue a civil case for compensation,” according to Epstein.

He believes Zygier was secretly jailed for revealing information to an Iranian in Melbourne in 2009 about operations he was involved in against Iran.

“It was this Iranian who played a key role in his downfall,” Epstein writes. “Put simply, Ben said too much to the wrong person at the wrong time.”

His conclusion contradicts a Der Spiegel investigation published last March, which claimed that Zygier had flown independently and unauthorized to Eastern Europe to try to turn a Hezbollah associate into a double agent in an apparent bid to impress his Mossad superiors.

“I just think it [the Hezbollah link] is not true,” Epstein said. “I couldn’t find any substantiation.”

But he rejects allegations that Zygier, who was a 34-year-old father of two when he committed suicide, was an extremist in one way or another. “The portrayal of him as either a zealot or traitor is not only wrong, it covers up the lack of transparency and simple care displayed by the governments of Australia and Israel.”

It was a “remarkable failure” by the Australian government that it did not “join the dots” connecting the timing of the assassination of Mahmoud al-Mabhouh in Dubai and Zygier’s arrest by the Shin Bet security service two days after the assassination made global headlines.

Mabhouh, a cofounder of Hamas’ military wing, was assassinated on January 19, 2010. Several Australian passports were used in the operation, prompting Australia to later expel Israel’s Mossad chief in Canberra.

The coincidence of the Dubai assassination and Zygier’s arrest “produced a chaotic nexus of recrimination, revelation and confusion,” Epstein writes.

“All of a sudden he [Zygier] gets ... jailed and no one in Australia makes the connection between the number one national security issue [passports] and Ben’s arrest,” he told Haaretz.

Epstein’s research revealed that three spy agencies were monitoring Zygier at the time: the Mossad, the Australian Security Intelligence Organization and the Iranians.

The book is about “Iran and not Hezbollah,” Epstein said. “It’s actually an inside view of the way journalism works. It’s also an explanation of how an Aussie ended up in Mossad.”

He concludes the book by writing: “It’s likely that few Israelis believe Ben deserved to die, but most seem to be willing to allow their government to punish their own, in secret.”

Will the truth ever emerge about what crime Zygier is alleged to have perpetrated?

“I do think we’ll find out because at some stage it’ll stop mattering,” Epstein said. “I’m not sure when that’ll be but someone has been wronged somewhere.”