A US soldier has killed more than a dozen Afghan civilians, many of them women and children, in a night-time shooting spree in southern Afghanistan.

The Afghan president, Hamid Karzai, condemned the shootings as "intentional murders" and demanded an explanation from the US.

The victims of the shootings, which left up to 16 civilians dead, included nine children and three women, Karzai's office said in a statement.

"This is an assassination, an intentional killing of innocent civilians and cannot be forgiven," Karzai said. He said he has repeatedly demanded the US stop killing Afghan civilians.

The White House said it was deeply concerned by initial reports of the incident and was monitoring the situation closely.

General John Allen, the top US commander in Afghanistan, issued a statement pledging a "rapid and thorough investigation" into the shooting spree, and said the soldier will remain in US custody.

Eleven members of one family who lived just a few hundred metres from the soldier's base in the Panjwai district of southern Kandahar province were killed when he broke into their compound after 3am and sprayed it with bullets, villager Ustad Abdul Halim said.

The father of the family, Wazir, and one child survived only because they were away from their home.

"Wazir and his young son were in Boldak district when it happened," Halim said by phone from the village, where survivors and government officials from nearby Kandahar city gathered to bury the dead.

The attacks took place in the villages of Balandi and Alkozai, and the US soldier went into three different houses and opened fire, Associated Press reported. The area is a former Taliban stronghold that has seen years of heavy fighting between insurgents and coalition forces.

It is not the first time US soldiers have intentionally killed Afghan civilians but the death toll is unprecedented for a single soldier. The soldier, who the Nato-led coalition said was arrested after the assault, appears to have made no attempt to cover up the shootings.

Allen, in his statement, offered his regret and "deepest condolences" to the Afghan people and vowed that he will make sure that "anyone who is found to have committed wrong-doing is held fully accountable".

"This deeply appalling incident in no way represents the values of [the International Security Assistance Force] and coalition troops or the abiding respect we feel for the Afghan people," said Allen. "Nor does it impugn or diminish the spirit of cooperation and partnership we have worked so hard to foster with the Afghan National Security Forces."

Caitlin Hayden, a spokeswoman for the White House National Security Council, said that President Barack Obama was briefed on the shooting incident. She said, "we are deeply concerned by the initial reports of this incident, and are monitoring the situation closely."

Anti-foreigner sentiment is already running high in Afghanistan after US troops burned copies of the Qur'an and sparked days of deadly protests. The burnings sparked violent protests and attacks that killed some 30 people. Six US service members have been killed in attacks by their Afghan colleagues since the Qur'an burnings came to light.

Sunday's killings risk rekindling that anger.

The coalition's deputy commander, Adrian Bradshaw, acknowledged there had been deaths, although he did not give a number.

"I cannot explain the motivation behind such callous acts, but they were in no way part of authorised ISAF military activity," he said in a statement. "An investigation is already under way and every effort will be made to establish the facts and hold anyone responsible to account."

Photographers at the burials saw the bodies of at least 15 bodies riddled with bullets. Halim put the death toll at 16, with others who were injured receiving treatment in a Nato military hospital.

Halim and another man from the village, Haji Satar Khan, said four people from the family of Fahed Jan, and one child from another family died in addition to the 11 members of Wazir's family.

The killings sparked a demonstration in the district, prompting the US embassy to warn residents and travellers in Kandahar to exercise caution.

Mokhtar Amiri contributed to this report