JERUSALEM (JTA) — Israel will pay more than $1 million to the family of Ben Zygier, a Mossad agent who committed suicide in an Israeli prison some three years ago.

Zygier, a Melbourne native, was arrested in January 2010 by Israel’s Shin Bet secret service and jailed in secrecy under the name Prisoner X until he took his life in an isolation cell in the Ayalon Prison 10 months later. The case was shrouded in secrecy until the Australian Broadcasting Corp. exposed Zygier’s identity in February.

“The reasons the state agreed to pay this sum stemmed from its desire to avoid a court hearing in which details that could harm national security might be revealed,” Israel’s Justice Ministry said in a statement released on Wednesday. The ministry said the payment was not an admission of fault for the suicide. Zygier’s family reportedly had accused Israel of negligence.

The money will be paid out over the next four years, according to Haaretz.

The agreement with the family, reached after extensive negotiations, contains a confidentiality clause.

Zygier’s family declined to speak to both Australian and Israeli publications, according to reports.

A prosecutor’s report released in April found that there was evidence that Zygier died after committing suicide as a result of failures by the Israel Prison Service, but that there was not enough evidence to bring criminal charges against the service or any of its personnel.

The case has not been closed, which means prison officials could still be charged with negligence in Zygier’s death at a later date.

The report also said that Zygier attempted suicide twice during his nine months in prison, saw three psychiatrists and met with social workers 57 times.