The U.S. Embassy in Islamabad declined to comment. The U.S. leads the coalition of NATO troops battling the Taliban in Afghanistan.
Drone strikes have been a growing source of friction between Islamabad and Washington. Khan and other officials regularly denounce the attacks as a violation of Pakistan's sovereignty, although the country's government is known to have supported some of the strikes in the past. The tension has further complicated a relationship that Washington views as vital to fight al-Qaida and the Taliban, as well as negotiate peace in Afghanistan.
The protest comes only two days after a rare U.S. drone strike outside of Pakistan's remote tribal region killed five people, including at least three Afghan militants, at an Islamic seminary in Khyber Pakhtunkhwa.
The attack outraged Pakistani officials, as did one on Nov. 1 that killed the former leader of the Pakistani Taliban, Hakimullah Mehsud, a day before the Pakistani government said it was going to invite him to hold peace talks.
Khan pushed the Pakistani government block NATO supplies after the strike on Mehsud, but it has shown little interest in doing so. Pakistani Prime Minister Nawaz Sharif has been a vocal critic of drone strikes, but he has also said he values the country's relationship with the U.S.
Sharif pushed President Barack Obama to end drone strikes in a visit to Washington in October, but the U.S. government has shown no indication that it intends to stop.
When Khan failed to persuade the Pakistani government to block NATO supplies earlier this month, he announced that he would hold a protest to do so himself.
Around 10,000 people participated in Saturday's protest. The protesters included members of Khan's party and two other parties that are coalition partners in the Khyber Pakhtunkhwa government. They shouted anti-U.S. slogans, such as "Down with America" and "Stop drone attacks."
"I am participating in today's sit-in to convey a message to America that we hate them since they are killing our people in drone attacks," university student Hussain Shah said. "America must stop drone attacks for peace in our country."
The federal information minister, Pervez Rashid, said the federal government's anti-drone stance was clear and accused Khan of "playing politics" on the issue.
Drone strikes are widely unpopular with Pakistan's public, both because they are seen as violating the nation's sovereignty and are believed to kill too many innocent civilians. Human rights organizations have said hundreds of civilians have died in the attacks, although the U.S. insists the number is much lower.
The land routes through Pakistan from the southern port city of Karachi to Torkham and another border crossing in southwest Baluchistan province have been key to getting supplies to NATO troops in Afghanistan. They now increasingly are being used to ship equipment out of Afghanistan as the U.S. seeks to withdraw most of its combat troops from the country by the end of 2014.
The routes have been closed in the past. The Pakistani government blocked the routes for seven months following U.S. airstrikes that accidentally killed two dozen soldiers on the Afghan border in November 2011. Pakistan finally reopened the routes after the U.S. apologized.
Also Saturday, militants kidnapped four school teachers who were working on a polio vaccination drive in Khyber's Sipah village, local government official Khurshid Khan said. Negotiations are underway for their release, he said.
Militants have killed more than a dozen polio workers and police protecting them over the last year. They claim the workers are spies and the vaccination is meant to make Muslim children sterile.
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Associated Press writers Munir Ahmed, Zarar Khan and Sebastian Abbot in Islambad contributed to this report.
