Sixteen Afghan civilians including three women and nine children have been shot dead in their homes by a rogue US soldier in a pre-dawn rampage.

President Hamid Karzai condemned the slaughter on Sunday as "unforgivable" and furiously demanded an explanation from Washington.

"When Afghan people are killed deliberately by US forces this action is murder and terror and an unforgivable action," Karzai said in statement.

Senior US officials were scrambling to determine what caused the soldier to go on a shooting spree after leaving his base in southern Afghanistan, apparently heavily-armed and carrying night-vision equipment.

Officials confirmed that the soldier was being detained in Kandahar and that the military was treating at least five wounded.