Ben Zygier, the Melbourne-born Mossad agent who committed suicide in his cell at Ramle’s Ayalon Prison in 2010, had been granted all the rights and protections due to him under Israeli law, a top Justice Ministry official told reporters on Thursday.

Even the unusual fact that his identity was kept secret was a security measure to which Zygier himself consented, the official said, recognizing that this was beneficial to national security and to his own and his family’s protection.

The official, who spoke on condition of anonymity, did not provide details of why Zygier was arrested, and what charges had been leveled against him. Avigdor Feldman, a defense lawyer who met with Zygier a day or two before he died, said the 34-year-old father of two had been charged with “serious criminal” offenses and faced long years in prison. Conflicting, unconfirmed reports have indicated that Zygier had spilled Mossad secrets to the Australian authorities or media, or was believed to have been about to do so.

The official said the state was considering filing negligence charges against those who failed to prevent his suicide on December 15, 2010. Although he was being held in a top-security jail cell under constant camera surveillance, and was reportedly considered a suicide risk, Zygier killed himself in the bathroom where there were no cameras, Israeli TV reported on Thursday evening. A transcript of the prison officials’ panicked call for medical assistance to Magen David Adom — “he’s hanged himself,” the caller reportedly wailed — was read out on Channel 10 news.

Feldman said Zygier was torn between accepting a plea bargain and a lengthy jail term, or risking conviction in a trial and a still longer term. He “absolutely” did not seem suicidal, Feldman said, but the lawyer noted that Zygier had been held in solitary confinement for eight or nine months, and that this could have a dramatic impact on a prisoner’s psyche.

The Justice Ministry official objected to the term “Prisoner X,” which was widely used at first to describe Zygier before his name became public knowledge, and said it created the false impression that Israel was some kind of dictatorship or Third World country that strips its citizens of their rights. Zygier had been granted all the rights afforded to him by law, including family visits and a fair judicial process.

“There are no Prisoner Xs in Israel,” said the official. “The allegation that Israel behaved like a dictatorship that makes people ‘disappear’ is nothing but irresponsible and malicious nonsense.” The official added that the entire process under which Zygier was held, and his case handled, was overseen by the most senior legal official in the judicial system. The gag order that prevented reporting of the matter was justified, the official added, noting that the affair’s exposure now had caused grave damage to national security.

Zygier’s family was notified as soon as he was arrested, he received legal representation, and he was granted family visits, the official said. He was being tried in a regular criminal proceeding, albeit behind closed doors.

According to reports, Zygier immigrated to Israel in 2000, was recruited by the Mossad, and worked for the agency for years, including heading a front company that sold electronics to Iran, a country he was said to have visited several times utilizing his Australian passport. Back in Australia in 2009, he was reportedly called in for questioning by Australian security authorities. He was arrested and jailed in Israel in early 2010.

The official did not rule out the possibility that ongoing restrictions on reporting the affair may be further eased, but also stressed that the state would seek equally comprehensive media blackouts in the future, in cases that pose a national security risk.

Official handling of the affair has been greatly criticized in the past few days, since Australian media broke the story. Knesset members used parliamentary privilege to bring the case to the public’s attention by asking about it during a Knesset session. One legislator said he had made a formal inquiry into the matter while Zygier was being held and was assured the matter was being properly handled. And an effort to persuade editors to suppress the story has been derided as anachronistic and heavy-handed.

Government officials and the military censor’s office, however, have argued that gag orders and other restrictions on the case have been necessary to minimize the damage to Israeli national security.