The battle for control of the city continued despite support from US-led special forces joining Afghan troops in efforts to push back the Taliban, who seized the city five days ago in a lightning strike.
With parts of the city still wracked with violence, and following claim and counter-claim by the Afghan government and the Taliban over who controlled the city, only a limited picture has emerged of conditions inside Kunduz.
"Afghan security forces are in control of Kunduz city," interior ministry spokesman Sediq Sediqqi told AFP.
"The clearance operation will take some time as Taliban remnants are firing from inside civilian houses and booby traps have been planted in places."
The Taliban sent mixed messages concerning their progress on Thursday, with spokesman Zabihullah Mujahid insisting that militant forces were holding their ground in the city.
But an Afghan Taliban commander who spoke to AFP from an undisclosed location said that Taliban fighters were conducting a strategic retreat from Kunduz.
Fighting raged all day, with columns of smoke visible over much of the city, it was hard to pinpoint which side had the upper hand.
Soldiers came under sporadic attacks from insurgents wearing Afghan security uniforms, many of whom took up positions inside residential homes.
Amnesty International condemned the Taliban's "reign of terror" in the embattled city, citing civilian testimonies of mass murder, gang rapes and house-to-house searches by militant death squads.
Civilians have paid a heavy price with the capture of Kunduz, the first provincial capital to fall to the militants since they were toppled from power in a 2001 US-led invasion of Afghanistan.
Precise losses in the fighting are not known but so far 49 bodies and more than 370 wounded people have been brought to the city hospitals, according to health officials.
The wounded included 64 children, medical charity Doctors Without Borders (MSF) said, adding that its trauma centre in Kunduz has been operating "beyond capacity".
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