Clinton made her sharpest comments during a three day diplomatic offensive in Pakistan, a U.S ally where she has generally praised Pakistan and its military for its willingness to take on the Taliban along its rugged frontier with Afghanistan.
In numerous encounters during her trip to Pakistan, Clinton has sought to counter widespread skepticism and even resentment over U.S. policy in the region by highlighting the broader U.S.-Pakistani relationship that goes beyond security concerns.
But during an interview with six top Pakistani editors, Clinton questioned the country's willingness to take on terrorists or help the U.S. track down to kill or capture al Qaeda leaders Osama bin Laden and Ayman Zawahiri.
Pakistan has long denied that there is proof that bin Laden and Zawahiri have found refuge in the lawless Pakistani region near the Afghan border.
"Al-Qaeda has had safe haven in Pakistan since 2002," Clinton said, referring the year U.S. forces invaded Afghanistan to topple the Taliban regime and attempt to capture bin Laden in the wake of the 9/11 terror attacks.
"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," she said. "Maybe that's the case, maybe they're not gettable. I don't know.''
She added, however, "As far as we know, they are in Pakistan."
In meetings with leaders, journalists, and ordinary citizens during her trip to Pakistan this week, Clinton has taken on criticism of U.S. foreign policy and accusations that the Obama administration is meddling in Pakistan's affairs.
"I am more than willing to hear every complaint about the United States" and "answer, but also to change where we can, so we that we do have better communication and we have better understanding,'' she told the editors.
"But this is a two-way street. If we are going to have a mature partnership where we work together," then "there are issues that not just the United States but others have with your government and with your military security establishment,'' Clinton said.
She was unapologetic for her frank talk.
"I don't believe in dancing around difficult issues because I don't think that benefits anybody," Clinton said. "I ask in the pursuit of mutual respect that you take seriously our concerns."
Earlier in her meeting with students at the Government College of Lahore, Clinton said the Pakistan had essentially ceded some of its territory to the Taliban and its terrorist allies.
"If you want to see your territory shrink, that's your choice," she said, adding that she believed it would be a bad choice.
Pakistan has been rocked by a series of terror attacks in recent weeks, most recently on Wednesday when more than 100 people died in a terror attack in Peshawar.
The terror offensive is meant as retaliation for a Pakistani military offensive against the Taliban that has taken over much of the South Waziristan province along the Afghan border.