WASHINGTON/GENEVA: US President Barack Obama on Wednesday apologised to Medecins Sans Frontieres for the deadly bombing of its hospital in Kunduz, Afghanistan, while the medical charity pressed its demand for an international commission to investigate what it calls a war crime.

MSF said that an independent humanitarian commission created under the Geneva Conventions in 1991 should be activated for the first time to handle the inquiry. Three investigations have already begun into Saturday's air strike that killed 22 people, including 12 MSF staff.

Obama telephoned MSF, or Doctors Without Borders, International President Joanne Liu to apologise and express his condolences, White House spokesman Josh Earnest said. Asked whether Obama offered some explanation to Liu, Earnest said no.

"He merely offered his heartfelt apology" and a commitment to find out what went wrong, he said.

Earnest said Obama told Liu that a US investigation would "provide a transparent, thorough and objective accounting of the facts and circumstances of the incident. And that, if necessary, the president would implement changes to make tragedies like this one less likely to occur in the future."

MSF said that the commission's inquiry would gather facts and evidence from the United States, NATO and Afghanistan, as well as testimony from MSF staff and patients who survived.

Only then would MSF consider whether to bring criminal charges for loss of life and partial destruction of its trauma hospital, which has left tens of thousands of Afghans without access to health care, it said.

"If we let this go, as if it was a non-event, we are basically giving a blank cheque to any countries who are at war," Liu told a news briefing in Geneva. "If we don't safeguard that medical space for us to do our activities, then it is impossible to work in other contexts like Syria, South Sudan, like Yemen."

Neither the United States nor Afghanistan were signatories to the International Humanitarian Fact-Finding Commission (IHFFC) but Jason Cone, executive director of MSF in the United States, called on Obama to consent to the commission.

"Doing so will send a powerful signal of the US government's commitment to and respect for international humanitarian law under rules of war," Cone said at a news conference in New York.

The White House said Obama had also called Afghan President Ashraf Ghani to express his condolences. The United States military took responsibility on Tuesday for the air strike, calling it a mistake.

Earnest said "there is no evidence that ... I've seen or that anybody else has presented that indicate that this was anything other than a terrible, tragic accident."

US Defence Secretary Ash Carter, speaking to reporters in Rome on Wednesday, said the investigation would "hold accountable anyone responsible for conduct that was improper."

HOSPITAL CHAOS

Liu spoke of the chaos as the bombs fell for an hour.

"Our patients burned in their beds, MSF doctors nurses, and other staff were killed as they worked. Our colleagues had to operate on each other," she said.

The Afghan Ministry of Defence said on Sunday Taliban fighters had attacked the hospital and were using the building "as a human shield", which the medical group denied, while pointing out it would be a war crime not to treat the wounded.

Liu said an impartial commission, which can be set up at the request of a single state under the Geneva Conventions that establish international standards for conducting war, was needed due to "inconsistencies between the US and Afghan accounts".

The United Nations has condemned the attack but said it would wait for the results of US, NATO and Afghan investigations before deciding whether to support an independent probe.

MSF's hospital in Kunduz had treated nearly 400 people, including some Taliban, wounded in heavy fighting in the days before the attack, MSF's Bruno Jochum said.

Its GSP coordinates had been shared with all authorities.

"We had eight ICU (intensive care unit) beds with ventilators, this was high-tech medicine. This was not the little bush hospital. You could not miss it," Liu said.

"Today we say enough, even war has rules."