The officer, who remains undercover, was a finalist for the job and would have become the first female chief of clandestine operations.
As one of the last remaining senior CIA officers who held leadership roles in the agency's interrogation and detention program, however, she was a politically risky pick.
Sen. Dianne Feinstein, the Senate Intelligence Committee's top Democrat, has criticized the interrogation program and personally urged CIA Director John Brennan not to promote the woman, according to a former senior intelligence briefed on the call.
Through a spokesman, Feinstein said she "conveyed my views to Mr. Brennan."
CIA spokeswoman Jennifer Youngblood said the assertion that the officer was passed over because of her involvement in the interrogation program was "absolutely not true."
More than a decade after it last used waterboarding, the CIA is still hounded by the legacy of tactics that America once considered torture. Brennan's ties to the interrogation program delayed for years his nomination to lead the CIA and Feinstein wants the agency to declassify a 6,000-page report on the interrogation program.
While many details about the program have become public, much is still shrouded in secrecy, making it impossible to evaluate its successes. Harsh interrogations led to some information, but also generated a lot of false information. And whether any of it could have been done without waterboarding, sleep deprivation and forcing people into small boxes is unknowable.
The officer briefly ran a secret CIA prison where accused terrorists Abu Zubayada and Abd al-Nashiri were waterboarded in 2002, according to current and former U.S. intelligence officials. She was also a senior manager in the Counterterrorism Center helping run operations in the war on terror.
She also served as chief of staff to Jose Rodriguez and helped carry out his order that the CIA destroy its waterboarding videos. That order prompted a lengthy Justice Department investigation that ended without charges.
Instead of picking the female officer, Brennan turned instead to the head of the CIA's Latin American Division, a former station chief in Pakistan who former officials said once ran the covert action that helped remove Serbian President Slobodan Milosevic from power. That program is regarded inside the CIA as a blueprint for running a successful peaceful covert action.
The former officials spoke on condition of anonymity because they were not authorized to discuss the CIA's operations publicly.
The name of the new head of the clandestine service is widely known in intelligence, diplomatic and journalistic circles, as is the name of the woman who was passed over. Both have declared their CIA affiliations with foreign governments around the world. The CIA, however, maintains that the names should not be made public because they are technically undercover.
Former acting CIA director John McLaughlin, who was part of the panel that helped select the next clandestine service leader, said the interrogation program "did not come up" in their discussions.
"The people moving into senior positions are extraordinarily accomplished and will do exception jobs," he said.
Women constitute nearly half of the agency's workforce but only about 30 percent of what is known as the Senior Intelligence Service. The CIA had determined that for every one woman achieving her SIS rank last year, four men got theirs.
"If the 2012 outcome were to be repeated in the coming years, such a trend would lead to diminishing representation of women at the senior ranks," according to a declassified CIA report.
In announcing his new clandestine chief, Brennan also promoted women to be his chief of staff and the agency's executive director.
"Women will hold fully half of the positions on his current leadership team," the agency said in a news release.
It is unclear what the female officer who was passed over will do next. She ran the CIA stations in London and New York.
"The officer chosen is a wonderful choice, and the woman not chosen was an equally wonderful choice," said former CIA Director Michael Hayden, who worked with both. "And I would hope that the agency can continue to make use of both of them in prominent leadership positions."
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