WASHINGTON, Nov. 4  The Bush administration signaled Sunday that it would probably keep billions of dollars flowing to Pakistan’s military, despite the detention of human rights advocates and leaders of the political opposition by Gen. Pervez Musharraf, the country’s president.

In carefully calibrated public statements and blunter private acknowledgments about the limits of American leverage over General Musharraf, the man President Bush has called one of his most critical allies, the officials argued that it would be counterproductive to let Pakistan’s political turmoil interfere with their best hope of ousting Al Qaeda’s central leadership and the Taliban from the country’s mountainous tribal areas.

Speaking to reporters in Jerusalem, Secretary of State Condoleezza Rice said that while the United States would “have to review the situation with aid,” she said three times that President Bush’s first concern was “to protect America and protect American citizens by continuing to fight against terrorists.”

“That means we have to be very cognizant of the counterterrorism operations that we are involved in,” she said. “We have to be very cognizant of the fact that some of the assistance that has been going to Pakistan is directly related to the counterterrorism mission.”