Steve Rodford stepped down as governor after five months
The resignation of the governor of HMP Maghaberry has been described as a "blow to the Prison Service".
Steve Rodford was appointed governor five months ago in the wake of criticism of prison staff after the death of a prisoner on suicide watch.
Mr Rodford's home address and car registration details were found in the cell of a dissident republican inmate at the County Antrim jail.
NI Prisoner Ombudsman Pauline McCabe said the reform agenda had to go on.
"It is deeply regrettable that Steve Rodford is leaving Maghaberry Prison," she said.
"In my view he is an excellent governor who did everything he could to bring creative thinking and a fresh perspective to the challenging task of implementing the recommendations of the Pearson Report (into the death of prisoner Colin Bell).
"Very careful thought now needs to be given to Steve Rodford's replacement and to the management and support arrangements that will enable a new Governor to take forward the urgently needed programme of change."
Ulster Unionist MLA Basil McCrea said the review of how prisons were run "must continue".
"Although I wish to extend my best wishes to the governor, I must admit that his resignation is a huge blow to the Prison Service who are currently undergoing a review in relation to reform," he said.
"Indeed, he had only been in post for a very short period of time when he ordered the first major search of the jail in more than 10 years - a most welcome move."
"With the departure of Mr Rodford we need to ensure that the review of how our Prison Service is run and managed continues."
Mr Rodford had recently been staying in a hotel
It is understood he moved out of his County Down home a number of weeks ago and had been staying at a hotel.
BBC Northern Ireland home affairs correspondent Vincent Kearney said Mr Rodford's wife was clearly "very alarmed".
"She moved back to England a number of weeks ago and made it clear she no longer wanted to live in Northern Ireland," he said.
"He felt he had no option, other than to step down.
"There has been a general threat against prison officers from dissidents for some time now."
Mr Kearney said that Mr Rodford's decision to step down was not just connected to the security threat against him.
He said there had been suggestions that Mr Rodford felt he was not able to implement the changes he believes were necessary to reform the regime at the jail.
Mr Rodford was appointed after a series of damning reports about the prison, which had been labelled one of the worst and most expensive prisons in the UK.
"When he was appointed by Prisons' Minister Paul Goggins, it was described as a watershed for the Prison Service," he said.
"He arrived from Whitemoor High Security Prison in England with a reputation as a tough but firm governor who wasn't afraid to make tough decisions.
"My understanding was that he quickly became disillusioned with the amount of bureaucracy and red tape in the system and felt he wasn't being given the support and operational independence that he believed he had been promised when he took the job.
"I have been told he expressed these concerns on a number of occasions in recent weeks and even if these potential threats from dissidents hadn't arisen, there was a strong possibility that at some point he may have resigned anyway."
SDLP policing spokesperson Alex Attwood said Security Minister Paul Goggins should make a public statement about the resignation.
"The prison system needs a Patten Report," he said.
"It needs root and branch change. Before and after devolution of justice, together with the reform of the Public Prosecution Service, the reform of prisons should have top priority."
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