That could spark a clash with the federal government.
The US Embassy in Islamabad declined to comment.
The US 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 US 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 November 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.
