WASHINGTON (AP) - One of the CIA's highest-ranking women, who once ran a CIA prison in Thailand where terror suspects were waterboarded, has been bypassed for the agency's top spy job. 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 challenged its supposed successes in a 6,000-page secret report. She 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." The officer briefly ran a secret CIA prison in Thailand 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. 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. 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. 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.