Afghan President Hamid Karzai condemns a shooting rampage by Western soldiers in southern Kandahar province on Sunday as "intentional murders".
But only one U.S. soldier appears to have been involved in the shootings, a U.S. official says.
Witnesses told Reuters they saw a group of U.S. soldiers arrive at their village in Kandahar's Panjwayi district at around 2 am, enter homes and open fire.
An Afghan minister earlier told Reuters that a lone U.S. soldier had killed up to 16 people when he burst into homes in villages near his base in the middle of the night.
"The incident that took place last night as a result 11 civilian killed in one house, four people killed in another house and in third house one killed four wounded as a result a total of Sixteen people killed and five wounded," said Afghan Tribal Affairs minister Asadullah Khalid.
Panjwayi district is about 35 km (22 miles) west of the provincial capital Kandahar city. The district is considered the spiritual home of the Taliban.
The incident comes just weeks after U.S. soldiers burned copies of the Koran at a NATO base, triggering widespread anti-Western protests, and plunging already strained U.S.-Afghan ties to a new low.
NATO's International Security Assistance Force (ISAF) said it had detained one of its soldiers and that an investigation was under way. It said the soldier reportedly went to more than one village near his base.
The Minister of Border and Tribal Affairs Asadullah Khalid, who is investigating the incident, said the soldier entered three homes, killing 11 people in the first one.
Civilian casualties have been a major source of friction between President Hamid Karzai's Western-backed government and U.S.-led NATO forces in Afghanistan.
The Afghan Interior Ministry condemned the shootings, which could intensify friction between Washington and Kabul as NATO prepares to hand over all security responsibilities to Afghans by the end of 2014, a process which has already started.
The Koran burning and the violence that followed, including a spate of deadly attacks against U.S. soldiers, tested brittle ties between the governments of Karzai and President Barack Obama and underscored the challenges that the West faces even as it moves to withdraw.
All foreign combat troops will withdraw by end-2014 from a costly war that has become increasingly unpopular.
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