The medical charity MSF says air strikes on its hospital in the Afghan city of Kunduz continued for more than 30 minutes after US and Afghan authorities were told of its location.
In a statement, MSF has condemned “in the strongest possible terms the horrific bombing of its hospital”.
MSF says the number of its staff killed has risen to nine, from three.
US forces were carrying out air strikes at the time. The Nato alliance has admitted the clinic may have been hit.
At least 37 people were seriously injured, 19 of them MSF staff. At least 100 patients were in the hospital.
Many patients and staff remain unaccounted for, MSF says.
The organisation says that all parties to the conflict, including Kabul and Washington, had been told the precise GPS co-ordinates of the hospital in Kunduz on many occasions.
A spokesman for US forces in Afghanistan, Col Brian Tribus, said: “US forces conducted an air strike in Kunduz city at 02:15 (local time)… against individuals threatening the force.
“The strike may have resulted in collateral damage to a nearby medical facility.”
The incident is being investigated, he added.
There has been intense fighting in Kunduz since Taliban fighters swept into the northern city on Monday.
Afghan officials said the government had regained control of Kunduz on Friday, but the Taliban denied the city had been retaken.
Eyewitnesses said they saw Taliban fighters on the streets or hiding in civilian houses.
Taliban leader Mullah Akhtar Mansour had described the seizure of Kunduz as a “symbolic victory”.
Kunduz, with a population of around 300,000, is one of Afghanistan’s largest cities and strategically important both as a transport hub and a bread-basket for the region.
The US-led Nato combat mission in Afghanistan ended in December 2014, but Nato forces remain for training purposes.
Nato’s Resolute Support Mission, which was launched in January 2015, consists of more than 13,000 troops from 42 countries. The US contributes around half of these.