US-led forces apologise to President Ashraf Ghani after 16 people including nine hospital staff were killed in Kunduz.

Doctors Without Borders (MSF) has said at least 16 people, including nine of its staff, have been killed in an overnight bombing of a hospital in the embattled Afghan city of Kunduz.

Among the fatalities in the early Saturday morning attack were three children. It also wounded 37 people, including 19 MSF staff, 18 patients and caretakers, according to the medical charity known for its French initials, MSF.

In a statement on Saturday, the office of President Ashraf Ghani said Army General John Campbell, head of the US-led forces in Afghanistan has apologised for the incident.

Officials of MSF earlier told Reuters that they “frantically phoned” NATO and Washington DC, as bombs rained on the hospital for “nearly an hour”.

The US-led coalition has also acknowledged launching the air strike “against individuals threatening the force”.

“The strike may have resulted in collateral damage to a nearby medical facility. This incident is under investigation.”

Earlier, NATO said that a US air strike “may have” hit the hospital, which is run by the medical charity, adding that the attack may have resulted in collateral damage.

The MSF hospital is seen as a key medical lifeline in Kunduz, which has been running “beyond capacity” in recent days of fighting which saw the Taliban seize control of the provincial capital for several days.

The trauma centre is the only medical facility in the region that can deal with major injuries.

“At 2:10 am [20:40 GMT] local time … the MSF trauma centre in Kunduz was hit several times during sustained bombing and was very badly damaged,” MSF said in a statement on Friday.

Deeply shocked at bombing of MSF hospital in #Kunduz. Staff and patients killed. MSF urges fighting parties to respect health facilities — MSF International (@MSF) October 3, 2015

At the time of the bombing, 105 patients and their caretakers and more than 80 MSF international and national staff were present in the hospital, the charity said.

Hospital coordinates know to US, Afghanistan

MSF said it gave the coordinates of the hospital to Afghan and US forces several times to avoid being caught in the crossfire.

“As MSF does in all conflict contexts, these precise locations were communicated to all parties on multiple occasions over the past months, including most recently on 29 September,” according to MSF Afghanistan representatives.

The bombing reportedly continued for more than 30 minutes after US and Afghan military offices in Kabul and Washington were first informed.

RELATED: Residents tell of suffering as battle for Kunduz rages

“MSF urgently seeks clarity on exactly what took place and how this terrible event could have happened,” MSF said.

After the attack, the medical charity urged all parties involved in the violence to respect the safety of health facilities, patients and staff.

Speaking to Al Jazeera, Taliban spokesperson Zabiullah Mujahid said that no Taliban fighters were present in the hospital at the time of the air strike.

“We condemn the bombing on the hospital. It was an attack carried out on innocent people.” Zabiullah told Al Jazeera.

“Our mujahidin [fighters] were not treated at the MSF trauma centre due to prevailing military conditions. Such attacks by US forces have taken place in Afghanistan for years now. This very attack has once again exposed the ruthless colors of the invaders to the Afghans,” he added.

MSF’s hospital is the only facility of its kind in the whole northeastern region of Afghanistan [MSF]

However, an Afghan interior ministry spokesperson claimed the fighters were attacking security forces with gunfire and grenades from an area near the hospital.

“According to our information, the Taliban were hiding in the hospital building and the area around it while attacking our forces,” Sediq Sediqqi said.

“We are assessing and evaluating the collateral damage to the medical facility. However, in any case, the safety of the civilians comes first,” the spokesman added.

A caretaker at the hospital, who was severely injured in the air strike, told Al Jazeera that clinic’s medical staff did not favour any side of the conflict.

“We are here to help and treat civilians,” Abdul Manar said.

“Several women and children are also killed in the strike. I could hear them screaming for help inside the hospital while it was set ablaze by the bombing. We are terrified and speechless.”

Battle for Kunduz

The development came a day after the Afghan government claimed it had successfully retaken parts of Kunduz from Taliban fighters, who had controlled the strategic city since Monday.

The Taliban, however, claimed it remained in control of most of Kunduz, our correspondent said.

Kunduz is facing a humanitarian crisis, with thousands of civilians caught in the crossfire between government forces and Taliban fighters.

Precise losses in the fighting were not known, but health authorities said on Friday that at least 60 people have been killed and 400 wounded.

As fighting spreads in neighbouring Badakhshan, Takhar and Baghlan provinces, concerns are mounting that the seizure of Kunduz was merely the opening gambit in a new, bolder Taliban strategy to tighten the grip across northern Afghanistan.

Afghan forces, backed by NATO special forces and US air strikes, have been going from house to house in Kunduz in a bid to flush Taliban fighters out of the city.

Al Jazeera’s Qais Azimy, reporting from Puli Khumri, about 130km from Kunduz, said heavy fighting was ongoing in the centre of Kunduz.

“Sources inside the city are reporting heavy clashes between the Taliban and the Afghan army. There is no set front line between the two sides, so the fighting is from street to street at the moment.

“People inside the city are suffering. There is a shortage of food, water and electricity,” our correspondent said.

The Taliban’s offensive in Kunduz, their biggest tactical success since 2001, marks a major blow for Afghanistan’s Western-trained forces, who have largely been fighting on their own since last December.

Civilian and military casualties caused by NATO forces have been one of the most contentious issues in the 14-year campaign against the Taliban, provoking harsh public and government criticism.

US-led NATO forces ended their combat mission in Afghanistan last December, though a 13,000-strong residual force remains for training and counterterrorism operations.

But there has been an escalation in air strikes by NATO forces in recent months despite the drawdown.

Additional reporting by Shereena Qazi. Follow her on Twitter @ShereenaQazi