Ambassador Eileen Donahoe told the council in Geneva on October 30 that Washington has serious reservations about human rights situation in Balochistan.
She said Pakistan Army operations there are "aimed at silencing dissent."
She said Pakistan should ensure that those guilty of torture, enforced disappearances, and extrajudicial killings must be prosecuted.
Donahoe made the remarks during Pakistan's Universal Periodic Review.
All UN members are expect to undergo such a review of their human rights record every four years.
Thousands of civilians, soldiers, and guerillas have been killed in eight years of unrest in the vast desert region where numerous ethnic Balochi factions are fighting for independence from Pakistan.