Hamid Karzai wants US forces out of Wardak province within two weeks, accusing them of fuelling instability.
A spokesman for Mr Karzai cited allegations of disappearances and torture by Afghans working under Americans control.
It comes just a week after the Afghan president ordered an end to local security forces calling in NATO air strikes amid concern over civilian casualties.
Presenter: Liam Cochrane
Speaker: Thomas Goutierre, Director of the Center for Afghanistan Studies at the University of Nebraska in Omaha
GOUTIERRE: Well I think we should understand that this is more of a situation relating to Afghan internal politics than it is the relationship between the United States and Afghan government. There's no question that this is going to make things a little more difficult in terms of the ultimate negotiations and the arrangements that are made for going forward relating to basing and things of that nature. But this particular province, which is very strategic, it's between Kabul and Kandahar, closer to Kabul, and the main road between those two cities goes right through it. It's also a relatively fertile and prosperous province in terms of its agriculture, but it's also one with diversity in its population. And right now the biggest questions relating to the Afghan National Army have to do with the diversity within that, or the lack of it particularly in places where it is stationed and where the majority of the military are not from the same ethnic group where they might be. This is a holdover from the unfortunate ethnic cleansing activities during the war with the Taliban and the civil war leading up to that.
COCHRANE: Well let's look at some of the specific allegations, what is it that is supposed to have happened under the Afghan forces control?
GOUTIERRE: Well and I don't have all of this latest information, but from what I've heard there were allegations of certain kinds of torturing. I haven't heard of the particular manner in which people might have been tortured. Also there have been allegations of inappropriate military exercises that have led to abuse of some individuals. So I don't have specifics relating to what kind other than the fact that the general conduct of the Afghan Special Forces in this particular region of this particular province has been out of order in terms of their military responsibilities, at least those are the allegations.
COCHRANE: How much accountability should be demanded from the US for the actions of the Afghan forces that are under their control?
GOUTIERRE: Well that's another part of the whole political equation, and I think ultimately the Afghans have to take responsibility for their own defence, and these kinds of things must be assumed by them, and they must be the ones who have to be responsible for any types of such allegations. The situation I think in terms of the American involvement there is just a further demonstration of how closely in the past our Special Forces have worked with Afghan Special Forces. And in that process there's strong relationships that are developed. But in this particular case obviously the Afghan Special Forces apparently have gotten out of control and to a degree there is I think at least on the minds of certain Afghans, guilt by association here. And it makes our task, the task of the international forces all the more complicated.