"The foreign minister conveyed to the secretary of state the deep sense of rage felt across Pakistan at the senseless loss of 24 soldiers due to the Nato/ISAF attack on the Pakistani post in Mohmand Agency," the statement said.
The incident "negates the progress made by the two countries on improving relations and forces Pakistan to revisit the terms of engagement," Khar said.
Nato helicopters and combat aircraft attacked two Pakistani military border posts in the restive Mohmand tribal region at 2 am yesterday.
The Pakistan army put the death toll at 24 though officials were quoted by the media as saying that 28 soldiers, including two officers, were killed in the air strike.
Pakistan-US relations, already strained by the May 2 American raid that killed Osama bin Laden in Abbottabad, plunged to a new low after the incident.
An emergency meeting of the Defence Committee of the Cabinet chaired by Prime Minister Yousuf Raza Gilani on Saturday night decided to cut off all Nato supply routes in Afghanistan and asked the US to vacate Shamsi airbase, which is reportedly used by CIA-operated drones.
The Foreign Office statement said Khar spoke to Clinton to inform the US administration of the decisions made by the Defence Committee of the Cabinet.
Khar told Clinton that attacks like the one in Mohmand tribal agency were "totally unacceptable".
"They demonstrate complete disregard for international law and human life, and are in stark violation of Pakistani sovereignty," Khar was quoted as saying.
"She informed secretary Clinton about the DCC decisions to stop Nato supply routes and that the US should vacate the Shamsi airbase within 15 days," the statement said.
Clinton condoled with Khar the loss of life in yesterday's incident.
"She said that she was deeply saddened by the event. She conveyed the US government's desire to work with Pakistan to resolve this issue," the statement said.
In a related development, foreign minister Ahmet Davutoglu of Turkey, a close ally of Pakistan, called Khar on Saturday night to express solidarity with the people and government of Pakistan in the wake of the Nato-ISAF attack.
Khar thanked Davutoglu and "condemned in the strongest terms the unprovoked and totally unacceptable attacks by Nato/ISAF which demonstrated complete disregard for international law and human life," said another statement from the Foreign Office.
Davutoglu assured Khar that Turkey, as a member of Nato, would ask for an impartial inquiry into the attack.