The American admission came after Human Rights Watch sent an open letter to US Defence Secretary Donald Rumsfeld, saying the US has failed to investigate or punish abuses by its soldiers. A US official said at least three deaths were still being investigated.
The HRW letter also claims that the US-run detention system in Afghanistan operates entirely outside the rule of law, and that commanders have repeatedly refused requests for visits by the Afghan Independent Human Rights Commission.
"It's time for the United States to come clean about crimes committed by US forces in Afghanistan," the BBC quoted Brad Adams, Asia Division director for Human Rights Watch (HRW), as saying.
A failure to prosecute soldiers for incidents in Afghanistan had led to "a culture of impunity" which may have spread to Iraq, he said.
The war in Iraq: Complete coverage