The Afghan president has ordered US special forces to leave Wardak province within two weeks.
The decision was being taken due to allegations of disappearances and torture by Afghans considered to be part of US special forces, said a spokesman for Hamid Karzai.
The strategically significant, central province of Wardak has been the recent focus of counter-insurgency operations.
A US statement said it took all allegations of misconduct seriously.
But the US could not comment specifically on this latest development "until we have had a chance to speak with senior government officials", the statement by a spokesman for US special forces said.
"This is an important issue that we must discuss with our Afghan counterparts," the statement said.
The Afghan president's office said the decision to order the expulsion of US special forces had been taken at a meeting of the National Security Council.
"After a thorough discussion, it became clear that armed individuals named as US special force[s] stationed in Wardak province engage in harassing, annoying, torturing and even murdering innocent people," it said.
"A recent example in the province is an incident in which nine people were disappeared in an operation by this suspicious force and in a separate incident a student was taken away at night from his home, whose tortured body with throat cut was found two days later under a bridge.
"However, Americans reject having conducted any such operation and any involvement of their special force. Continue reading via BBC...