Later that day, a statement from an Israeli court appeared to publicly confirm details about the case for the first time.
The statement, released by the court in the partial lifting of the gag order, described a "prisoner who was both an Israeli citizen and a foreign national."
"The inmate was registered under a false identity for security reasons, but his family was notified immediately upon his arrest," the statement said.
The court document also said that the prisoner was found dead in his cell two years ago and that a judge ordered an investigation into his death.
The death was recently ruled a suicide, the statement said, and authorities are investigating whether there was negligence in the case.
Additional details cannot be revealed "for reasons of state security," the document said.
Lawyer: I spoke with prisoner shortly before his death
Human rights lawyer Avigdor Feldman said he met with the prisoner a day or two before he allegedly committed suicide.
At the time, Feldman said, the prisoner had not been tried or convicted but was indicted and in pretrial imprisonment.
"His wife asked me to go and see him and look into some legal questions which he had," Feldman said.
Feldman said he met with the prisoner "as a lawyer who was asked not really to represent him but to consider his legal options. It's quite common."
Feldman said that while he was not aware of the details of the cell, "it is supposed to be suicide-proof."
When asked why the prisoner was being held and reports about his dealings with Iran, Feldman answered, "I can't comment unless you want to come and visit me in prison."
One journalist shares his story
Most people worldwide first learned Prisoner X's name as news of the case surged this week.
But journalist Jason Koutsoukis said that an Australian intelligence source first told him about Ben Zygier in October 2009.
The intelligence source, Koutsoukis told CNN, identified Zygier and two other Australian citizens who were also Israeli citizens.
"(The source) suggested to me that they had been involved in a passport scam -- a means to change their identities in Australia and use the new travel documents they obtained to be able to go into countries that were sensitive for Israel," Koutsoukis said.
That issue was a particularly contentious topic between Australia and Israel in 2010, around the time when Zygier was reportedly detained.
Authorities in the United Arab Emirates at the time said that fake Australian passports had been used by three suspects who slipped into a Dubai hotel and killed a Hamas leader. And media and intelligence reports said Israel's Mossad was behind the attack.