Jami Miscik, deputy director for intelligence, told her staff Tuesday she will be resigning, a U.S. official said, speaking on condition of anonymity. The official didn't comment whether she resigned voluntarily or was asked to step down.
At least five other top agency officials have resigned since Goss, a former congressman who chaired the House Intelligence Committee, became CIA director in September. Goss has appointed his former House aides to top positions.
The changes have raised concerns among some lawmakers and others that Goss was purging intelligence professionals and replacing them with political appointees.
But Goss' supporters say he is bringing needed changes to an agency that has been widely criticized for failing to prevent the Sept. 11, 2001, terror attacks and for its faulty intelligence on Saddam Hussein's weapons programs in Iraq.
Given the turnover at the agency, Miscik's departure was largely expected.
The Los Angeles Times reported that Miscik head the department that erroneously reported Iraq possessed large stocks of chemical and biological weapons.
One former official, speaking on condition of anonymity, told the Times that her departure "wasn't handled in a particularly classy fashion."
"It's understandable that a new CIA director would want to have his own team," the former official told the newspaper. "But it's unfortunate they're losing somebody like Jami, who in most circumstances would be exactly the kind of person you would want to have to solve problems."
Miscik joined the CIA in 1983 as an economic analyst working on Third World debt issues, according to her biography on the CIA Web page. She was named deputy director in May 2002, making her responsible for CIA analysis and the preparation of the president's daily intelligence briefing.
The New York Times said Miscik, in a message to subordinates, described her resignation as part of a "natural evolution" and that every intelligence chief "has a desire to have his own team in place to implement his vision and to offer him counsel."
The newspaper first reported the resignation on its Web page in a story that said former intelligence officials who spoke on condition of anonymity said she was forced to resign.
Among the officials who have stepped down is John McLaughlin, who served as acting director following the resignation of George Tenet. McLaughlin retired, citing personal reasons.
In addition to the shake-up at the CIA, U.S. intelligence operations are being overhauled as a result of a new law creating a national intelligence center and a powerful new position of national intelligence director to oversee 15 agencies.