"A lot of things are put down to family reasons," Mr Little said, describing Mr Fletcher's departure as a surprise. "He certainly seemed to be well in control and very keen on the job just before Christmas. Now he's going and there's reference to the review coming up."
He suggested the Government could be planning to merge the GCSB with the domestic spying agency, the Security Intelligence Service (SIS), which might have unsettled the director.
Mr Fletcher was not available for interview yesterday.
The search is now on for his replacement. An acting director will be appointed at the end of February.
Rebecca Kitteridge, Director of the Security Intelligence Service, could be a contender for the director's job.
Opposition parties yesterday urged a more transparent process than Mr Fletcher's appointment in February 2012. It was revealed Mr Fletcher was an old school friend of Prime Minister John Key.
Mr Fletcher came into the job immediately after the GCSB-assisted raid on internet entrepreneur Kim Dotcom, later found to be illegal.
A review found up to 88 New Zealanders might have been illegally spied on by the agency, after which the Government reformed spy laws to make it legal to spy on Kiwis to prevent cyber attacks.
This prompted widespread debate about the scope of surveillance in New Zealand, which was reignited by whistleblower Edward Snowden last year.
Ian Fletcher
• Began career as diplomat with New Zealand Ministry of Foreign Affairs after gaining postgraduate degree in history
• Held senior positions in British civil service, including head of the Home Civil Service, and later worked for the United Nations in Kosovo
• After a stint in Australian civil service, he was appointed GCSB head in February 2012
• Led GCSB during a difficult period, when agency was found to be spying illegally on New Zealanders including Kim Dotcom
• Oversaw major reforms of GCSB which allowed the agency to spy on NZers.
• Defended GCSB amid revelations by whistleblower Edward Snowden