Pressure is mounting on Washington over the apparent US air strike on an Afghan hospital that killed 22, an incident the Pentagon chief says is "confused and complicated" but which medical charity Doctors Without Borders has branded a war crime.

The charity, which goes by its French initials MSF, said on Sunday it has closed the trauma centre, seen as a lifeline in a war-battered region with scant medical care, and demanded an independent probe into Saturday's devastating air raid.

President Barack Obama has promised a full investigation but the international outrage over the deadly incident has piled pressure on Washington for a more transparent probe.

"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 on Monday.

Stokes also hit out at claims by Afghan officials that insurgents were using the hospital as a position to target Afghan forces and civilians.

"These statements imply that Afghan and US forces working together decided to raze to the ground a fully functioning hospital with more than 180 staff and patients inside because they claim that members of the Taliban were present," he said.

"This amounts to an admission of a war crime. This utterly contradicts the initial attempts of the US government to minimise the attack as 'collateral damage'."

The group said Afghan and coalition troops were fully aware of the exact location of the hospital, having been given GPS coordinates of the facility which had been providing care for four years.

NATO said US forces carried out the bombardment in the "vicinity" of the hospital to protect American special forces on the ground who came under enemy fire, but MSF said the surrounding area was largely unscathed.

The charity said 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.

US Defense Secretary Ashton Carter expressed sadness over the "tragic loss of life" but warned that the investigation will not be swift.

"The situation there is confused and complicated so it may take some time to get the facts, but we will get the facts, but we will be full and transparent about sharing them," he told reporters on a flight to Madrid at the start of a European tour.

However MSF's Stokes stressed the need for an independent probe, saying "an internal investigation by a party to the conflict would be wholly insufficient".