KABUL: Afghan troops have regained control of the main square in Kunduz, a strategic northern city briefly seized by Taliban insurgents last week that has been the scene of intense fighting, officials said Wednesday.

During the fight to retake the city, a United States (US) airstrike destroyed a hospital run by Doctors Without Borders, killing at least 22 people.

Read: US military air strike hits MSF hospital in Kunduz

The international charity on Wednesday called for an independent 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.

"Afghan forces have control of Kunduz city, however some scattered elements of the enemy are still hiding in the residential areas inside people's houses," deputy spokesman Zafar Hashemi said.

"This could at times slow down the speed of our military operations as we put the utmost effort into not harming civilians."

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.

Read: 'Northern Afghan city of Kunduz collapses into hands of Taliban'

After sealing the city and mining roads, they looted and burned government buildings and businesses, and harassed journalists and women's and human rights workers.

The government launched its counter-offensive on Thursday, and troops have since fought intermittent running battles with insurgents, who have launched attacks on security forces from the rural outskirts of the city, officials and residents have said.

Authorities Wednesday had no precise casualty figures, though the number of dead and wounded is believed to be in the hundreds.

Sarwar Hussaini, the spokesman for the Kunduz provincial police chief, said Wednesday 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.

The security situation remains fluid, however, with fighting on the outskirts of the city in recent days.

Residents said militants have regrouped in the Chahar Dara district to the west, where they have had a presence for some months.

Bilal Ahmad, a grocer, said he hesitated to open his shop because of the tenuous situation. He said tanks have moved into the main square.

Doctors Without Borders, known by its French acronym MSF, meanwhile called for the first-ever fact-finding mission to be launched under the Geneva Conventions.

MSF's international president, Joanne Liu, told reporters in Geneva that the strike "was not just an attack on our hospital, it was an attack on the Geneva Conventions. This cannot be tolerated."

Liu said MSF is "working on the assumption of a possible war crime," but said the group's real goal is to establish facts about the incident and the chain of command, and clear up the rules of operation for all humanitarian organisations that work in conflict zones.

The commander of US and the North-Atlantic Treaty Organisation (Nato) forces in Afghanistan, Gen. John F. Campbell, said Tuesday that the strike was a mistake, and investigations are underway.