US Defence Secretary Leon Panetta says a video which appears to show US Marines urinating on the corpses of Afghans is "utterly deplorable".
Those who had taken part in the incident would be held accountable "to the fullest extent", he said.
The video, which was posted online, purports to show four US Marines standing over the bodies of several Taliban fighters, at least one of whom is covered in blood.
The origin of the video is not known.
Mr Panetta said he had ordered the commander of US and Nato forces in Afghanistan to investigate the incident.
"I have seen the footage, and I find the behaviour depicted in it utterly deplorable," he said in a statement.
The US authorities say they are still checking the authenticity of the video, but the BBC's Steve Kingstone in Washington says senior officials have wasted no time in going into damage limitation mode.
Our correspondent says the alleged incident is deeply embarrassing for a US administration that had promised to project a more sensitive image of American military power.
There has been anger in the Taliban stronghold of Kandahar at a video appearing to show US troops urinating on the dead bodies of insurgents in Afghanistan.
The latest incident comes as America tries to encourage talks between insurgents and the Afghan government ahead of US troop withdrawal.
Kandahar resident Tawab Khan said he thought the treatment of the corpses was against Islam and that it was the role of the international community to act. He called for an investigation by the Human Rights Commission and the arrest of those involved.