French Defense Minister Jean-Yves Le Drian said "hundreds" of militants have been killed since French troops arrived in the African country at the request of its government, CNN reported.
"From the moment our forces, supported by Malian forces, began missions and patrols around the towns which we have taken, we have encountered residual jihadist groups which fight," Drian said during a radio interview.
French Foreign Minister Laurent Fabius said some French troops will remain in Mali to flush out militants in "terrorist havens" in northern Mali.
France's ground-and-air campaign in its former colony sent Islamic fighters who seized the northern region into the desert. Northern Mali fell during the chaotic times that followed a military coup.
The Islamic extremists imposed Sharia law and banned music, smoking and drinking, among other activities. They also destroyed historic tombs and shrines.
French-led troops control Timbuktu and Gao, along with an area between the two cities that was an insurgent stronghold for nearly a year, CNN said. Troops are working to secure Kindal, the last major city under militant rule.
French officials said there are 4,000 French soldiers in Mali fighting alongside nearly 3,800 African soldiers.
Fabius said France has "no intention" of staying in Mali, The New York Times reported.
"It is the Africans and the Malians themselves [who must] guarantee the security, the territorial integrity and the sovereignty of the country," he said.