A secret military operation in early 2005 to capture senior members of Al Qaeda in Pakistan’s tribal areas was aborted at the last minute after top Bush administration officials decided it was too risky and could jeopardize relations with Pakistan, according to intelligence and military officials.

The target was a meeting of Qaeda leaders that intelligence officials thought included Ayman al-Zawahri, Osama bin Laden’s top deputy and the man believed to run the terrorist group’s operations.

But the mission was called off after Donald H. Rumsfeld, then the defense secretary, rejected an 11th-hour appeal by Porter J. Goss, then the director of the Central Intelligence Agency, officials said. Members of a Navy Seals unit in parachute gear had already boarded C-130 cargo planes in Afghanistan when the mission was canceled, said a former senior intelligence official involved in the planning.