In a series of public appearances on the final day of a three-day visit, Clinton was pressed repeatedly by Pakistani civilians and journalists about the secret U.S. program that uses drones to launch missiles to kill terrorists.
But she refused to discuss the drones strikes along the porous border area with Afghanistan that have killed key terror leaders but also scores of civilians.
Clinton's visit was rocked from the start by a devastating terrorist bombing in Peshawar that killed 105 people, many of them women and children. Her tour has proceeded tensely, revealing clear signs of strain between the two nations despite months of public insistence that they were on the same wavelength in the war on terror.
What is less apparent is what U.S. officials are aiming for with Clinton's tough new comments about Pakistani officials' failure to eliminate al-Qaida as a threat within their borders.
Pakistan's military recently launched a major offensive in the South Waziristan border area to clear out insurgent hideouts. But two earlier army efforts made little progress there - leaving questions about the military's resolve to tackle al-Qaida head-on.
Clinton carefully scaled back her comments from a day earlier suggesting that some Pakistani officials knew where al-Qaida's upper echelon has been hiding and have done little to target them.
When the U.S. gathers evidence that al-Qaida fugitives are hiding in Pakistan, Clinton said Friday during a Pakistani media interview, "We feel like we have to go to the government of Pakistan and say, somewhere these people have to be hidden out."
"We don't know where, and I have no information that they know where, but this is a big government. You know, it's a government on many levels. Somebody, somewhere in Pakistan must know where these people are. And we'd like to know because we view them as really at the core of the terrorist threat that threatens Pakistan, threatens Afghanistan, threatens us, threatens people all over the world," Clinton said.
And during an interview Friday on ABC's "Good Morning America," Clinton demurred when asked if she thought Pakistan was harboring terrorists, saying: "I don't think they are. ... But I think it would be a missed opportunity and a lack of recognition of the full extent of the threat, if they did not realize that any safe haven anywhere for terrorists threatens them, threatens us, and has to be addressed."
A day earlier she was more explicit in her skepticism, telling a Pakistani journalist in Lahore: "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. Maybe that's the case. Maybe they're not gettable. I don't know."
A top Pakistan official insisted Friday his country is fighting back against militants and also urging the world to do more against the rise of terrorism.
"There was a time when the world was telling us to do more," Interior Minister Rehman Malik acknowledged, speaking Friday alongside Clinton at a police training center.
"We have decided to fight back," he said. Malik did not explicitly refer to Clinton's comments, but his words appeared intended to counter what she said.
Late Thursday, Pakistani army officers displayed two passports seized from a suspected terror hideout in South Waziristan and believed linked to terror operatives.
Asked repeatedly Friday about the U.S. use of drones, a subject which involves highly classified CIA operations and is rarely acknowledged in public by American officials, Clinton said only that "there is a war going on." She added that the Obama administration is committed to helping Pakistan defeat the insurgents.
Clinton said she could not comment on "any particular tactic or technology" used in the war against extremist groups in the area.
The use of the drone aircraft, armed with guided missiles, is credited by U.S. officials with eliminating a growing number of senior terrorist group leaders this year who had used the tribal lands of Pakistan as a haven beyond the reach of U.S. ground forces in Afghanistan.
During an interview with Clinton broadcast live in Pakistan with several prominent female TV anchors, before a predominantly female audience of several hundred, one member of the audience said the Predator attacks amount to "executions without trial" for those killed.
Another asked Clinton how she would define terrorism.
"Is it the killing of people in drone attacks?" she asked. That woman then asked if Clinton considers drone attacks and bombings like the one that killed more than 100 civilians in the city of Peshawar earlier this week to both be acts of terrorism.
"No, I do not," Clinton replied.
Another man told her bluntly: "Please forgive me, but I would like to say we've been fighting your war."
Clinton was to fly to Abu Dhabi in the Persian Gulf for a meeting Saturday with Palestinian President Mahmoud Abbas.