Afghan Special Forces (SF) recaptured the center of the northern Kunduz province on Thursday after fierce clashes with Taliban militants, forcing the insurgents to retreat amid heavy street battles that were still underway.

Residents said soldiers were conducting house-to-house searches and had removed the Taliban flag from the central square, replacing it with government colors.

Special Forces launched an operation at about 9pm on Wednesday alongside soldiers and police. They were backed by international Special Forces, believed to be acting mainly in an advisory role.

“By 3.30am, our special forces were able to retake the city and clear the city from terrorists,” said Sediq Sediqqi, spokesman for the Afghan interior ministry. He said: “There are lots of dead bodies of Taliban in the city right now. Hundreds of them.”

Interior ministry spokesman noted the battle is a joint army and police operation and that roadblocks set up by the Taliban to prevent any movement had been removed. He said essential supplies, including food and medicine, would be delivered soon to the residents.

He added around 200 Taliban fighters have been killed in the fighting so far but did not provide a figure for government casualties. Kunduz police chief, Sarwar Hussaini, said bodies of dead Taliban fighters lay on some of the city’s streets but that the clearance operation was complicated because some Taliban fighters had hidden inside people’s homes.

However, residents remaining inside Kunduz and hunkering down at their homes said they could still hear explosions and shootings outside.

A Taliban spokesman denied the government had retaken Kunduz, saying insurgent fighters were still resisting in the centre and controlled most of the rest of the city.

The recapture of parts of Kunduz follows three days of heavy fighting after the Taliban seized the city in a surprise assault. It was the first time since 2001 the insurgents managed to breach a large city. They did so despite being vastly outnumbered. Thousands of security forces simply fled when the militants advanced.

At least 30 people, mostly civilians, had been killed in the fighting as of Wednesday, according to a tweet from health ministry spokesman Wahidullah Mayar. He also said hospitals in Kunduz had treated about 340 injured.

The Taliban’s recent gains in Kunduz and neighboring provinces highlight that a large and strategic patch of northern Afghanistan is imperiled by a rapidly expanding insurgency.

The three days it took to bring a major city back under government control may have political consequences for President Ashraf Ghani, whose first year in office has been clouded by infighting and escalating violence around the country.