Lieutenant General Michael Flynn, who had served as director of the DIA since July 2012, and deputy David Shedd, said in a joint memo to employees that "they will depart the agency and retire by early Fall 2014," according to an agency statement yesterday.
Their "retirements have been planned for some time," said Pentagon press secretary Rear Admiral John Kirby in an email.
Flynn played a key role in the wars in Iraq and Afghanistan, serving under General Stanley McChrystal as part of US efforts to dismantle insurgent networks through raids by special operations forces.
The DIA is undergoing dramatic changes under a plan to deploy more spies in the field, and Flynn's efforts to speed up the transformation proved "disruptive," according to his critics, the Post reported.
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US defence officials, who spoke on condition of anonymity, rejected the report and said Flynn and Shedd both had planned to retire for a number of months.
The intelligence agency's statement said the pair had led a "transformation" that "helped reshape DIA culture," allowing "the agency to nimbly respond to recent crises without having to create special task forces or move people."