Afghan President Hamid Karzai has given US special forces two weeks to leave the strategically important Wardak province.
He acted on Sunday after allegations that Afghans working with US forces are torturing and abusing other Afghans.
The decision seemed to have taken occupation forces by surprise.
However, the US has frequently angered the Afghan public over issues ranging from Korans burned at a US base to allegations of civilian killings.
"We take all allegations of misconduct seriously and go to great lengths to determine the facts surrounding them," the US forces claimed in a statement.
Also on Sunday, a series of attacks in eastern Afghanistan showed insurgents remain on the offensive even as coalition forces prepared to end their combat missions by the end of 2014.
Suicide bombers targeted Afghanistan's intelligence agency and other security forces in four co-ordinated attacks in the heart of Kabul and outlying areas in a bloody reminder of the insurgency's reach nearly 12 years into the war.
Presidential spokesman Aimal Faizi said that the decision to order US special forces out of Wardak had been taken during a meeting of the national security council because of the actions of Afghan groups who are considered to be linked to them.
He said that all special forces operations were to cease immediately in the restive province next to Kabul, which is viewed as a gateway to the capital and has been the focus of counterinsurgency efforts in recent years.
"Those Afghans in these armed groups who are working with the US special forces, the defence minister asked for an explanation of who they are," Mr Faizi said.
"These individuals should be handed over to the Afghan side so that we can further investigate."
A statement by the security council said that the armed individuals have been "harassing, annoying, torturing and even murdering innocent people."
Mr Faizi said the issue had already been brought up with the coalition.
A US statement said only that the announcement was "an important issue that we intend to fully discuss with our Afghan counterparts."
If you appreciated this article then please consider donating to the Morning Star's Fighting Fund to ensure we can keep developing your paper.
Defence Secretary Philip Hammond believes himself vindicated by the High Court ruling that his Iraq Historic Allegations Team (IHAT) is independent.
A look at the causes and possible outcomes of Silvio Berlusconi and his right-wing coalition's lead in the polls.
Attacks such as yesterday's horrific murder in Woolwich didn't happen before the 'war on terror.' It's time we recognised the consequences of the conflicts we've unleashed