At a news conference concluding three days of meetings, Clinton said Washington has told the Pakistani government what it believes about the location of al Qaeda leaders on its soil.
"With respect to the location of those who were part of the planning and execution of the attack of 9/11 against our country, we firmly believe that a significant number of them are in the border area of Pakistan," she said when asked about the U.S. view.
"We are actively looking for additional information that would lead us to them," she added.
The Pakistani government denies that al Qaeda leader Osama bin Laden and his senior lieutenants are hiding in its territory.
Bin Laden is believed to have fled into Pakistan from Afghanistan weeks after the U.S. military invaded Afghanistan in October 2001 in retaliation for the 9/11 attacks.
Clinton spoke from a news conference in New Delhi, where she touted prospects for, despite sharp differences on carbon emissions, as they readied a pact giving U.S. companies more access to India's expanding markets.