The officer, a former Marine who is under cover and whose first name is Greg, was recently the head of the Special Activities Division, the CIA's elite paramilitary force.
He has twice been station chief in Afghanistan, where in December 2001 he jumped to shield Karzai when the US military accidentally bombed the position of the man who would become Afghanistan's president.
He earned Karzai's trust, and the Obama administration asked him to troubleshoot the fraught relationship with the Afghan leader in 2012, when he again served as station chief in Kabul.
He was identified in the 2007 memoir of former CIA Director George Tenet as "Greg V." According to Tenet, he identified Karzai as the only credible Taliban opponent from Afghanistan's southern region and urged that he be protected.
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The new chief replaces Frank Archibald, who abruptly resigned as director of the clandestine service earlier this month after telling colleagues he opposed a major reorganization of the CIA being contemplated by Director John Brennan.
One idea under consideration by Brennan would break down the walls between the agency's spying and analysis arms, combining operations officers and analysts in "centers" devoted to specific subjects.
The centers would be modeled after the Counter Terrorism Center, which oversees the drone killing program and is seen as one of the few success stories in what has been a difficult decade for American "HUMINT," or human intelligence.
Such centers could focus on cyber warfare, China, or other subjects that now fall under multiple disparate elements of the sprawling spy agency.
"The former Director of NCS announced last week that he planned to retire from the agency after a long and distinguished career at CIA," CIA spokesman Ryan Trapani said in a statement.