Washington is seeking to build the Pakistani state and its economy as a way to wean the country from Islamic extremism.
Yet the Al Qaeda organization remains the "most clear and present danger to US security," Director Michael Hayden said in a speech Thursday.
The Pentagon hopes better ties will strengthen NATO and boost the mission in Afghanistan.
A surge by the US and its allies is needed in the country.
Foreign Relations Committee hearing comes a day after the release of two critical reports.