During the fight to retake the city, a US airstrike destroyed a hospital run by Doctors Without Borders on Saturday, killing at least 22 people. The international charity today called for a fact-finding mission to determine whether the strike violated the Geneva Conventions.
A spokesman for President Ashraf Ghani said some "scattered elements of the enemy" remain in residential areas of Kunduz as operations continue to clear the Taliban from the city.
He added that Ghani has ordered the continuation of operations to "fully clean the city, province and the entire northeastern region of terrorist groups."
Taliban fighters seized control of Kunduz city, capital of the province of the same name, for three days last week. After sealing the city and mining roads, they looted and burned government buildings and businesses, and harassed journalists and human rights workers.
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Sarwar Hussaini, the spokesman for the Kunduz provincial police chief, said today the government had regained control of the main square, which had traded hands several times, with each side tearing down the other's flag and hoisting its own.
"The national flag is flying over the main square, shops have re-opened and life is returning to normal," he said, adding that main roads running east and south have opened and traffic is starting to flow.
Emergency relief supplies of food and medicines had not been able to reach the city until Wednesday, leading to dire shortages, residents and medical officials said.