Distraught and furious Afghans vowed vengeance yesterday after a US soldier apparently walked from a Nato base into the homes of civilians, turning his weapon on the families inside and killing 16 people, nine of them children.

The Afghan Ministry of Interior has urged people to show restraint until investigators have completed their inquiry, but concerns are mounting that the incident will re-ignite violent protests that swept Afghanistan last month after US servicemen burnt copies of the Koran at Bagram Air Base, north of Kabul.

Nazim Shah returned to his home in Panjwai district from a trip to Kandahar to find his entire family killed. Sobbing into the phone, he told The Independent: "All my family is dead ... We will get revenge on those who killed my family. We won't let this rest easily." The attack comes at a crucial time, as President Hamid Karzai and US officials, under strained relations, negotiate a future role for foreign forces after Nato troops hand over security to Afghan forces in 2014.

Witnesses and officials gave differing accounts of yesterday's events, but it appears that the soldier, as yet unnamed, left the joint US-Afghan Zangebad base at about 3am. He walked to the villages of Balandi and Alkozai, about a kilometre away, and began the killings which left nine children, three women and four men dead. Five more were wounded.

"The US soldier attacked three different houses, killing 11 people in the first house, four in the second house and one in the third house," said Mahammad, a tribal elder in Panjwai. "The 11 people who were first shot dead were brought together in one home and the soldier put pillows, sticks and blankets on them and burnt them." Photographs of the victims showed burn injuries.

General Carsten Jacobson, spokesman for the Nato-led International Security Assistance Force (Isaf), confirmed the soldier went back to the base and gave himself up, and was in detention.

A US official said the suspect is a conventional soldier from Joint Base Lewis-McChord, Washington state. The soldier was assigned to support a special operations unit of either Green Berets or Navy Seals engaged in a village stability operation.

American officials were swift to try to limit the damage, with the US commander in Afghanistan, General John Allen, issuing a statement pledging a "rapid and thorough investigation" with anyone found to have committed wrongdoing to be held "fully accountable".

President Barack Obama, who telephoned Mr Karzai to express his condolences and vow to hold those responsible to account, said: "This incident is tragic and shocking, and does not represent the exceptional character of our military and the respect that the United States has for the people of Afghanistan."

Mr Karzai sent a high-level delegation from the ministries of defence and interior, the National Directorate of Security and the National Security Council to investigate. He called the killings "an intentional act" against civilians.

Nato officials will now have to wait to see whether the promise of investigations will be enough, or whether the incident will spark another round of retribution and bloodshed. Haji Aghalalai Dastgiri, an elder from Panjwai and a member of Kandahar's provincial council, told The Independent: "People have been gathering to discuss this. They will probably approach the Kandahar governor's office to discuss this with him. If he does not provide a satisfactory response, people may protest in the streets."

Samad Khan, a farmer who said he lost all 11 members of his family, said villagers would demand the Americans hand over the shooter – a demand that will not be met – before deciding what action to take. "This is an anti-human and anti-Islamic act," said Mr Khan. "Nobody is allowed, in any religion in the world, to kill children and women."

Mr Dastgiri said witnesses said the soldier had "appeared drunk". Most described the shooting as the work of a single man, although some reports said more than one soldier was involved. The Taliban claimed "50 civilians [were] martyred by American terrorists" and called the incident an "act of genocide".

The US embassy in Kabul tweeted a warning to people in Kandahar. Last month, after US servicemen accidentally burned Korans, 30 Afghans were killed in demonstrations, six Isaf soldiers were killed by members of the Afghan security forces who turned on them in apparent revenge, and two US military advisers were shot dead.

In 2010, in Kandahar province, a group of US soldiers murdered at least three Afghans and collected their body parts as trophies. Eleven soldiers were convicted on various charges.

Timeline: inflammatory actions that sparked a year of violence

20 March 2011

Florida Pastor Terry Jones douses a Koran in kerosene and sets fire to it after a mock trial. There is a violent backlash in Afghanistan and at least 14 people, including seven UN workers, are killed in the city of Mazar-e-Sharif, as well as 10 others in Kandahar.

7 January 2012

An Afghan investigative commission accuses the US military of abuse at the Parwan detention centre outside Bagram airbase. President Karzai demands that the US turns over all suspected militants to Afghan custody and free those being held without evidence.

11 January 2012

A video emerges showing what is believed to be four US Marines urinating on the corpses of three Taliban fighters. President Hamid Karzai condemns the actions as "completely inhuman" and Pentagon officials promise a criminal investigation.

8 February 2012

Eight young Afghans are killed in a Nato bombing in Kapisa province. The government releases gruesome photographs of the dead boys, seven of whom it says are aged between six and 14 and one around 18. Nato later admits the mistake, describing it as "very sad".

20 February 2012