At the same time, she said, the Obama administration would like to have an end to safe heavens in Pakistan.

She, however, appeared to tone down tempers between the two countries which has reached a new peak after Admiral Mike Mullen, Chairman of the Joint Chiefs of Staff, told a Congressional Committee that the Haqqani network is a veritable arm of Pakistani spy agency ISI.

"I would certainly urge people to look at the entirety of Admiral Mullen's testimony. He did raise serious questions, which our government has raised with the Pakistanis about the continuing safe haven for terrorists that strike across the border in Afghanistan against Afghans, Americans, NATO, ISAF troops, civilians working there, as well as within Pakistan."

"But Admiral Mullen also said that this is a very critical consequential relationship. We have a lot of interests that are in common, most particularly the fight against terrorism," Clinton argued.

"So we are certainly making clear that we want to see an end to safe havens and any kind of support from anywhere for terrorists inside Pakistan, and we also want to continue to work to put our relationship on a stronger footing," Clinton told reporters at a joint press availability with visiting Nigerian Foreign Minister Olugbenga Ashiru.

Clinton said Uzbekistan has been very helpful to us with respect to the Northern Distribution Network.

"They have also been helpful with Afghanistan in terms of reconstruction. They are deeply involved in assisting Afghans and the Afghan Government to try to rebuild and make Afghanistan a more prosperous, peaceful country," she said.

"We believe that our continuing dialogue with officials of the government is essential. It always raises, as I have and as others from our government continue to do so, our concerns about human rights and political freedoms," she said.

"But at the same time we are working with the Uzbeks to make progress, and we are seeing some signs of that, and we would clearly like to deepen our relationship on all issues," Clinton said.