US Secretary of State Hillary Clinton has questioned Pakistan's commitment to hunt top Al-Qaida leadership hiding inside the country and accused it of failing to track them down.

"Al-Qaida has had safe haven in Pakistan since 2002... I find it hard to believe that nobody in your government knows where they are and couldn't get them if they really wanted to," Clinton told a group of senior Pakistani journalists in Lahore on Thursday.

"Maybe that's the case, maybe they're not gettable. I don't know... As far as we know, they are in Pakistan," she said in unusually blunt remarks during a visit to Pakistan that is aimed at mending fences and improving strained ties.

Clinton's comments  made when a journalist asked why the war on terror has focused so much on Pakistan  reflected concerns expressed recently by senior American diplomats, including Ambassador Anne Patterson.

She also alluded to the role of Pakistan's powerful ISI agency, which has been accused of secretly supporting the militant groups.

In a remark that appeared aimed at the ISI, she said: "If we are going to have a mature partnership where we work together there are issues that, not just the US, but others have with your government and with your military security establishment."