Medical charity MSF said Sunday it has shut down operations in the Afghan city of Kunduz after an apparent US bombing raid on its hospital, demanding an independent investigation into what it labelled a war crime.

Doctors Without Borders (MSF) said 22 people were killed, some of whom burned to death in their beds as the bombardment continued for more than an hour, even after US and Afghan authorities were informed the hospital had been hit.

It is the only medical facility in the whole northeastern region of Afghanistan that can deal with major war injuries. Its closure, even temporarily, could have a devastating impact on local civilians.

"The MSF hospital is not functional anymore. All critical patients have been referred to other health facilities and no MSF staff are working in our hospital," Kate Stegeman, a spokeswoman for the charity, told AFP.

Stegeman said she could not confirm whether the trauma centre will reopen.

The charity condemned the "abhorrent" bombings, demanding answers from US-led NATO forces in Afghanistan.

"Under the clear presumption that a war crime has been committed, MSF demands that a full and transparent investigation into the event be conducted by an independent international body," MSF general director Christopher Stokes said.

MSF said Afghan and coalition troops were fully aware of the exact location of the hospital, having been given GPS co-ordinates of a facility which had been providing care for four years.

It added that despite frantic calls to military officials in Kabul and Washington, the main building housing the intensive care unit and emergency rooms was "repeatedly, very precisely" hit almost every 15 minutes for more than an hour.

Afghan officials said insurgents were using the hospital building as a position to target Afghan forces and civilians.

But MSF denied any combatants were present in the facility, adding that "not a single member of our staff reported any fighting inside the hospital compound prior to the airstrike".

MSF said some 105 patients and their caregivers, as well as more than 80 international and local MSF staff, were in the hospital at the time of the bombing.

"The bombs hit and then we heard the plane circle round," said Heman Nagarathnam, MSF's head of programmes in northern Afghanistan.

"There was a pause, and then more bombs hit. This happened again and again. When I made it out from the office, the main hospital building was engulfed in flames.

"Those people that could had moved quickly to the building's two bunkers to seek safety. But patients who were unable to escape burned to death as they lay in their beds."

The hospital's main building was completely gutted and some bodies of those trapped inside were charred beyond recognition.

The dead included 12 MSF staff and 10 patients, among them three children.

US President Barack Obama offered his "deepest condolences" for what he called a "tragic incident".

"The Department of Defense has launched a full investigation, and we will await the results of that inquiry before making a definitive judgement as to the circumstances of this tragedy," Obama said.

But MSF's stokes said: "Relying only on an internal investigation by a party to the conflict would be wholly insufficient."

NATO earlier conceded US forces may have been behind the bombing, after its forces launched a strike which they said was intended to target militants.

The incident has renewed concerns about the use of US air strikes in Afghanistan, a deeply contentious issue in the 14-year campaign against Taliban insurgents.

UN rights chief Zeid Ra'ad Al Hussein earlier also called for a full and transparent probe, noting: "An air strike on a hospital may amount to a war crime."

"This event is utterly tragic, inexcusable and possibly even criminal," he said.

The air raid came five days after Taliban fighters seized control of the strategic northern city of Kunduz, in their most spectacular victory since being toppled from power by a US-led coalition in 2001.

Afghan forces, backed up by their NATO allies, claim to have wrestled back control of the city.

MSF's withdrawal from Kunduz comes as the region grapples with a humanitarian crisis, with food and medicine shortages affecting thousands of civilians caught in the crossfire between government forces and insurgents.

At least 60 people are known to have died and 400 to have been wounded in the past week's fighting.

"Such attacks against health workers and facilities undermine the capacity of humanitarian organisations to assist the Afghan people at a time when they most urgently need it," the International Committee of the Red Cross said.