Pakistan's protest came after a U.S. drone strike Sunday in Waziristan.
The strike killed three suspected militants who were hiding out in an abandoned girls school, according to U.S. officials. There were no other casualties.
Drones strikes have become increasingly unpopular in Pakistan. Earlier this month, lawmakers here established a new set of guidelines for rebuilding the country's relationship with the United States. Among their first conditions was the immediate cessation of all drone strikes in Pakistani territory.
Today's harsh condemnation is the latest in a series of tit-for-tat accusations that have soured Pakistan-U.S. relations ever since the May 2011 Navy SEAL raid that killed al Qaeda leader Osama bin Laden.
Relations hit a new low last November when a U.S. airstrike killed 24 Pakistani soldiers in Solala, along the country's Afghan border. U.S. officials said the attack was a mistake, but stopped short of issuing a formal apology. In response, Pakistan closed the NATO supply route from its side of the Khyber Pass into Afghanistan, cutting off supplies desperately needed to support the Afghan mission.
Recently, there had been signs that both sides were willing to compromise. Marc Grossman, U.S. special envoy to the region, recently wrapped up a two day visit to Pakistan, during which he met with Pakistani Prime Minister Yousuf Raza Gilani and Pakistan's foreign minister to lobby for the reopening of the route. Pakistani officials themselves say they want the route re-opened, but have set the cessation of drone strikes and a formal apology for the Solala incident as preconditions.