Coalition forces killed 15 civilians in a shooting spree in Afghanistan's southern Kandahar province on Sunday, the defence ministry said, in an incident likely to deepen the growing divide between Washington and Kabul.

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.

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 defence minister ... is deeply shocked and saddened by the killings of 15 innocent civilians and the wounding of nine more at the hands of the coalition forces, the ministry in Kabul said in a statement.

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.

I cannot explain the motivation behind such callous acts, but they were in no way part of authorized ISAF military activity, ISAF deputy commander Lt. Gen. Adrian Bradshaw said in the statement.

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.

(Reporting by Ahmad Nadem in Kandahar and Hamid Shalizi in Kabul; Writing by Amie Ferris-Rotman, Editing by Dean Yates)