"Nothing has changed our efforts to go after terrorists, and nothing will change those efforts," Panetta said in response to questions about CIA missile attacks, launched from unmanned Predator aircraft.
Although he refused to discuss details of the attacks, the Washington Post quoted Panetta as saying that efforts begun under the Bush administration to destabilize al-Qaeda and destroy its leadership "have been successful."
"I don't think we can stop just at the effort to try to disrupt them. I think it has to be a continuing effort, because they aren't going to stop," Panetta said at his first news briefing since taking up the job.
The CIA has launched about three-dozen Predator strikes in Pakistan since late last summer, two of them during the Obama administration.
Panetta's comments came as senior Pakistani and Afghan leaders held lengthy talks here with each other and with their U.S. counterparts.
The talks, quickly arranged during the first overseas trip of special U.S. envoy Richard C. Holbrooke this month, include the foreign and defense ministers of both countries, along with Afghanistan's interior minister and Pakistan's intelligence chief.
The Pakistani army chief of staff is also here on a separate visit to his U.S. military counterparts.
Relations between Pakistan and Afghanistan have long been marked by mutual suspicion. Pakistan believes Afghanistan is too close to India, Islamabad's historical adversary to the east, while Afghanistan suspects that Pakistan has continued its traditional support for the Taliban.
Panetta has voiced concerns about Pakistan's recently announced truce with local Taliban leaders in that country's Swat Valley region, and noted that similar agreements with militant groups in the past had allowed al-Qaeda to strengthen its base.