CIA Director John O. Brennan announced new agency leaders Tuesday, including giving the directorship of National Clandestine services to a longtime officer who served in Pakistan and Africa and was recently in charge of the agency's Latin America division, The Washington Post reported.
The CIA confirmed the appointment but said reports the female officer's ties to the interrogation program influenced the decision were untrue.
"The assertion she was not chosen because of her affiliation with the CT [counter-terrorism] mission is absolutely not true," CIA spokeswoman Jennifer Youngblood said.
The female officer led the National Clandestine Service on an interim basis in the past two months and was considered a front-runner. However, she faced opposition because of her role in an interrogation program critics said relied on torture to get information from al-Qaida captives after the Sept. 11, 2001, attacks on the United States.
The Post said she also ran a secret prison in Thailand where two detainees were subjected to waterboarding and other harsh techniques and later helped order the destruction of videotapes of the sessions.
Youngblood said the new National Clandestine Service chief is a "talented and effective intelligence officer ... known for his collaborative and inclusive leadership style."
She said women will fill two other senior CIA jobs.
The female officer was expected to return to her role as deputy of the clandestine service, the Post said.
Brennan faced a harsh confirmation hearing over his own ties to the interrogation program.
The names of both officers are known in the intelligence community, but the agency asked that their identities not be revealed because they are working undercover, the Post said.
A former senior CIA official, speaking on the condition of anonymity, told the Post women at the agency "will be outraged" the female officer was passed over.
"She is very popular. She is an excellent officer and very good administrator," the official said.