The us military is investigating whether a U.S. AC-130 gunship – which was in the area firing on Taliban positions to defend USA special operations troops there – is responsible for the bombardment, a USA military official said on condition of anonymity.
Medecins Sans Frontieres said at least nine of its staff were killed in the attack.
MSF said all parties to the conflict in Afghanistan were clearly informed of the precise location, via Global Positioning System coordinates, of its facilities.
Medical charity Doctors Without Borders (MSF) said it was treating 59 children at its trauma centre in Kunduz which is running “beyond capacity”.
It said the bombing continued for more than 30 minutes after American and Afghan military officials were first alerted they were being hit.
“MSF urgently seeks clarity on exactly what took place and how this awful event could have happened”, the statement said.
Defense Secretary Ash Carter expressed condolences to the families of those killed in the crash.
Sixty people were killed and 400 wounded in the fighting since Monday.
Along with other private contractors and North Atlantic Treaty Organisation troops, the U.S. soldiers are focusing on training Afghanistan’s national security forces.
The USA military has carried out a number of air strikes this week in support of government forces in Kunduz, the provincial capital and the fifth largest city in Afghanistan.
The hospital was “partially destroyed” in the bombing, and 30 people were “unaccounted for”, the group said. “Among the 80, 15 were worldwide staff. All of them are safe… but unfortunately three of the Afghan staff members, they were among the casualties”.
“Kunduz city is burning”, Kunduz lawmaker Fatima Aziz said through tears.
Most of the wounded were being transferred to another hospital in Puli Khumri, about two hours away.
The crash comes with Afghan forces battling the Taliban which has blighted the country since the 2001 US-led invasion of Afghanistan.
Al Jazeera’s Qais Azimy, reporting from Puli Khumri, about 130km from Kunduz, said the bombing injured at least 50 people.
The worldwide Committee of the Red Cross said the strike was “an appalling tragedy”. At the time of the attack it had 105 patients, with 394 treated in the past week.
“I could hear sounds of heavy gunfire, explosions and airplanes throughout the night”, said Khodaidad, who has only one name.
The U.S. Embassy released a statement recognizing the “difficult humanitarian situation” in Kunduz and praising MSF’s work.
MSF doctors treat all people according to their medical needs and do not make distinctions based on a patient’s ethnicity, religious beliefs or political affiliation.
In a statement, the Taliban accused “barbaric American forces” of deliberately carrying out Saturday’s strike, which “killed and wounded tens of doctors, nurses and patients”.