Afghan president Hamid Karzai has given US special forces two weeks to leave Wardak province in the centre of Afghanistan.
Afghan soldiers with the US troops are accused of being behind disappearances and torture.
The US said it took all allegations seriously but could not comment on this issue "until we have had a chance to speak with senior government officials".
A statement by President Karzai’s office said the incidents have caused resentment amongst the Afghan public.
"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.
"The meeting strongly noted that such actions have caused local public resentment and hatred."