Group says it controls most of Afghan city after it was briefly taken by government forces backed by US air strikes.

The Taliban has reportedly regained control of large parts of the northern city of Kunduz, after days of intense fighting against Afghan troops backed by US air strikes, Al Jazeera has learned.

Earlier on Sunday, government forces, which have been trying to take control of the city, said they had made gains, but those appear to have been short-lived.

Al Jazeera’s Qais Azimy, reporting from Puli Khumri just south of Kunduz, said that at around 12:00 GMT, Taliban fighters launched counter-attacks, driving back government forces from the areas, where they had earlier made gains.

Residents in Kunduz have told our correspondent that more than 100 people have died, but exact figures are hard to arrive as those dead and injured are stuck in their homes due to the fighting.

Images also showed streets of the city strewn with dead bodies.

Related: MSF medical charity leaves Kunduz after air strike

“It is a very fragile situation. Afghan security officials are telling us that they are suffering from lack of leadership and coordination,” he said.

Even with the deployment of 7,000 troops, our correspondent said, the government is still unable to retake the strategic city.

In a big jolt to the government of President Ashraf Ghani, the Taliban launched an attack and captured the strategic northern city on Monday.

“They are also telling us that they are moving slowly because they claim the Taliban fighters are hiding in residential areas. They said they want to avoid civilian casualties, so they have to do a door-to-door search.”

A Kunduz resident, who just escaped the city to Puli Khumri, also confirmed to Al Jazeera that Taliban fighters have taken over civilians homes and have refused to let residents leave.

Independent probe

The news comes as the medical charity group Doctors Without Borders (MSF) announced that it had withdrawn from the city, after an apparent US air strike that killed 13 of its staff and 10 patients.

Kate Stegeman, the communications manager for the group known by its French acronym, MSF, said all critical patients have been referred to other health facilities and no MSF staff are working in the hospital.

“Some of our medical staff have gone to work in two hospitals where some of the wounded have been taken.”

In a separate interview, Bart Janssens, MSF director of operations, said that as of Sunday, there is “still no explanation why this attack happened”.

“Our building has been completely destroyed,” he told Al Jazeera.

Late on Sunday, MSF General Director Christopher Stokes issued a statement calling for an independent 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,” he said.

US Defense Secretary Ash Carter also issued another statement on Sunday saying, his office “will get the facts” of the incident.

RELATED: US investigates Afghan hospital air strike

MSF has denied that any fighters were present in the hospital, although Janssens said that it is “possible” that some of those who were being treated were wounded fighters.

Aminullah, a Kunduz resident, told Al Jazeera that all of the doctors were moving to Kabul or Mazar-e-Sharif, fearing for their lives.

His three children and wife “haven’t eaten for the past three days. We don’t even have a water supply. My children are falling sick and I don’t know where to take them”, he said.

“Forget about getting medical treatment, no one is able to even provide coffins for the dead bodies in the city.”

The charity said that despite frantic calls to US and Afghan military officials in Kabul and Washington, the attack continued.

In a statement released by the White House on Saturday, President Barack Obama offered his “deepest condolences” for what he called a “tragic incident”.

Meanwhile, Al Jazeera has learned that at least seven doctors have arrived in Kunduz from capital Kabul to help with the patients at the regional hospital there.

Earlier on Sunday, Al Jazeera’s Azimy said that only three doctors were taking care of at least 500 patients.