Pakistan said US forces shot dead two of its soldiers and wounded another on in an incident near the Afghan border.
A senior Pakistani official told Reuters the US forces mistook the Pakistani patrol for al Qaeda or Taliban fighters.
"It was due to some misunderstanding," the official said, speaking on condition of anonymity.
Pakistan was the main supporter of Afghanistan's former Taliban regime until the September 11th, 2001, suicide attacks on the United States, when it chose to back US efforts to drive the fundamentalists from power.
A statement from the Pakistani military's public relations department said a strong protest had been lodged with the US authorities about the incident.
It said US forces opened fire on the Pakistani patrol at 5 a.m. GMT at a border post in tribal Waziristan region, some 260 km southwest of the capital Islamabad.
The statement did not give any explanation for the shooting, the first such reported incident involving US troops operating in Afghanistan.
Pakistani forces and Afghan soldiers, assisted by a US-led coalition, patrol their own sides of the border which runs along a remote tribal belt where remnants of the ousted Afghan Taliban regime and al Qaeda network are believed to be hiding.
Pakistan and Afghanistan are trying to settle a row over the poorly defined 2,450 km border, with the United States mediating.
Relations between Kabul and Islamabad worsened in recent weeks with Afghan officials accusing Pakistani forces of intruding into Afghan territory, a charge strongly denied by Pakistan.