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Secretary of State Hillary Rodham Clinton, on a visit meant to improve relations with Pakistan, strongly suggested Thursday that some Pakistani officials bore responsibility for allowing al-Qaida terrorists to operate from safe havens along this country’s frontier.

“I find it hard to believe that nobody in your government knows where they are, and couldn’t get to them if they really wanted to,” she said to a group of Pakistani journalists on her second day here. “Maybe that’s the case; maybe they’re not gettable. I don’t know.”

It is extremely rare for an official of Clinton’s rank to say publicly what American politicians and intelligence officials have said in more guarded ways for years. The remarks upset her hosts, who have had hundreds of soldiers and civilians killed as Pakistan has taken on a widening campaign against certain militant groups that have threatened the state from the country’s tribal areas.

But they gave voice to the long-time frustration of U.S. officials with what they see as the Pakistani government’s lack of resolve in rooting out not only al-Qaida but also the Taliban leadership based in Quetta, and a host of militant groups that use the border region to stage attacks on U.S. and NATO forces in Afghanistan.

Clinton’s statement was only one of several pointed remarks on issues ranging from security to poor tax collection during a day in which she ran into a wall of distrust and mostly hostile questioning in public appearances intended to soothe relations, suggesting she was no longer willing merely to listen to Pakistan’s grievances.

The shift in tone came after a meeting with university students in which she expressed regret about past injustices in the U.S.-Pakistani relationship, as well as about the disputed American presidential election in 2000, which she said showed that all democracies are flawed.

“We have to decide if we want to move beyond the past in your country and in our country,” Clinton declared. “We are now at a point where we can chart a different course.”

Rarely in her travels as secretary of state has Clinton encountered an audience so uniformly suspicious and immune to her star power as the polite, but unsmiling university students that challenged her at Government College University in this edgy Pakistani city.

In a later exchange with American journalists, Clinton did not try to temper her remarks, saying they would contribute to a healthier, more open relationship with Pakistan. But the U.S. ambassador, Anne W. Patterson, sought to put them in a broader context of efforts to persuade the government to root out militants in its frontier regions.

“We often say there needs to be a focus on finding these leaders,” Patterson said. “Most of al-Qaida is in South Waziristan,” the frontier area near Afghanistan where the Pakistani army is conducting a campaign against militants.

Clinton’s comments were prominently played on Pakistani news channels, and government officials rejected her assertion.