WASHINGTON (CNN) -- The undercover officer temporarily running the CIA's spy division who had ties to the agency's controversial interrogation program will not get the job permanently.
CIA Director John Brennan said on Tuesday the first female to lead the National Clandestine Service will be replaced by a man, a nearly 30-year veteran who served covertly overseas, including a stint as station chief in Pakistan.
The identifies of these undercover officials were not made public.
Whether the acting director would get to keep the job was in question due to opposition from a number of senior lawmakers concerned about her ties to the CIA's controversial interrogation and detention program.
After the September 11, 2001, attack, sources familiar with her career said she was assigned to the CIA's Counter Terrorism Center, where she was involved in the effort to track down and capture suspected al Qaeda terrorists.
She moved to the clandestine unit as chief of staff when her boss at the time, Jose Rodriguez, was tapped to run the service in 2004.
According to the sources, the two were involved in a decision to destroy 92 videos of interrogations at overseas clandestine prisons that involved the use of harsh techniques on some of the terror detainees including waterboarding and stress positions.
The destruction infuriated many members of Congress who believe the techniques were torture and prompted a Justice Department investigation that did not result in charges.
Brennan faced stiff questions about the interrogation program at his confirmation hearing in March. Now as CIA director, he is responsible for providing the agency's response to a 6,000 page Senate Intelligence Committee report that concluded the CIA exaggerated how effective those interrogations were in providing actionable intelligence.
Brennan took the unusual step of asking three former senior CIA officials to review the candidates for the head of the clandestine service, which included the well-respected interim director.
Critics suggested he was looking for political cover because of the interrogation controversy.
CIA spokesman Todd Ebitz denied the acting director's counter terrorism efforts played a role in the decision to name someone else to run the clandestine service.
"The assertion she was not chosen because of her affiliation with the CT mission is absolutely not true," Ebitz said.
In addition to the new NCS Director, Brennan named a minority officer to serve for the first time as the third-ranking officer at the agency. Meroe Park will be the executive director running the day to day activities of the CIA.
Deb Bonk also has been tapped to be Brennan's chief of staff.