This Feb 15. 2013 file photo shows the tombstone of Ben Zygier at Chevra Kadisha Jewish Cemetery in Melbourne, Australia. (Andrew Brownbill/AP)

Israel denied Tuesday that a reputed Australian-Israeli agent of its Mossad spy agency who committed suicide in secret custody in 2010 had contact with Australian intelligence services.

The statement from Prime Minister Benjamin Netanyahu’s office is the first time Israel has named the reported spy, Ben Zygier, who had been widely referred to as Prisoner X, though the statement shed no light on the murky circumstances of his arrest.

According to Australian news media reports, Zygier, 34, was jailed after disclosing details of Mossad’s operations to the Australian intelligence service, which was investigating him on suspicion of using his Australian passport to spy for Israel.

But the Israeli statement denied that. “The Prime Minister’s office stresses that the late Mr. Zygier had no contact with the Australian security agencies,” it said.

Netanyahu’s office asserted that there was “excellent cooperation” between the Israeli and Australian governments and security agencies, as well as “full coordination and complete transparency in dealing with current issues.”

The statement appeared to be an attempt to smooth over tensions with Australia, which said it would ask Israel for an explanation for Zygier’s death in a maximum-security cell 10 months after he was arrested.

The case was kept secret by Israeli authorities for more than two years under a sweeping gag order before it was reported last week by the Australian Broadcasting Corp. The revelations have caused a furor in Israel, with some parliament members demanding an official inquiry.

According to the results of an Israeli inquest into Zygier’s death, released Tuesday by the Justice Ministry, he hanged himself in the bathroom of his cell using a rolled wet sheet tied to the bars of a window.

At 8:19 p.m. Dec. 15, 2010, “the deceased was found hanging in the shower room inside Cell 15 with a sheet around his neck that was tied to the window of the bathroom,” according to the declassified record of a court ruling on the inquest.

A forensic examination found a small amount of sedative in Zygier’s blood, suggesting that he was under some form of medical treatment.

Rejecting a request by state lawyers to close the case, the presiding judge found that wardens responsible for keeping watch on the prisoner had failed to follow monitoring procedures. She recommended that the state attorney’s office consider prosecuting those involved, including senior officials in the Israeli prisons service, noting that the evidence suggested that they were culpable.

Israeli officials have not disclosed what accusations Zygier faced, but a lawyer who visited him said that he had been charged with grave security crimes and that he had been weighing an offer of a plea bargain.

Australian news reports said Zygier had been investigated by the Australian intelligence service on suspicion of using his Australian passport to spy for Mossad, traveling to Lebanon, Syria and Iran. A report Monday by the Australian Broadcasting Corp. said Zygier had disclosed details of Mossad operations to Australian intelligence officers, including plans for a top-secret mission in Italy. He was arrested by his Israeli handlers on suspicion of revealing the information, the report said.