After clashes in Konna, most opted to relinquish control of towns and disappear into the desert.
France launched its operation last Friday, after the Islamists seized Konna and began advancing further south.
France sent troops at Mali's request after Islamists seized the strategic town of Konna on January 10.
French and Malian forces retook the key town of Konna from militants Friday, a French source said.
The central town of Konna has since been recaptured, the Malian government says.
BBC: UK troops to assist Mali operation to halt rebel advance
Its armed forces have been helping government forces in the West African country recapture the central town of Konna.
Hundreds of French troops have been deployed in Mali, both in the conflict zone near Konna and in the capital, Bamako.
BBC: Hollande steps up France security over Mali and Somalia
It was confirmed that French jets had made air strikes as Islamist rebels were forced out of the town of Konna.
BBC: French soldier killed and hostage feared dead in Somalia
One of Ansar Dine's lieutenants, Iyad Ag Ghaly, was killed in the fight over the central town of Konna, security sources said.
One of the group's lieutenants, Iyad Ag Ghaly, was killed in the fight over the central town of Konna, security sources said.
Konna, the city recaptured, was the de facto line of government control.
Eleven Malian soldiers have also been killed and 60 injured in fighting around Konna, Malian interim President Dioncounda Traore said in a statement.
BBC: Hollande steps up France security over Mali and Somalia
French involvement began the day after militants said January 10 that they had seized the city of Konna, east of Diabaly in central Mali.
Residents in Mopti, just south of Konna, told the BBC they had seen French troops helping Malian forces prepare for a counter-offensive against the Islamists.
BBC: French troops continue operation against Mali Islamists
Late on Friday Malian officials said they gained control of Konna.
Additionally, a French helicopter pilot died while taking part Friday afternoon in an aerial operation targeting a terrorist group moving on the town of Mopti, near Konna, Le Drian said.
"Konna is under our control this evening but we are still conducting mopping-up operations, " said Lt Col Diarra Kone, though he warned that some rebels might still be in the town.
He also revealed that a French helicopter pilot, Lieutenant Damien Boiteux, was killed in Friday's fighting - during an air raid to support Mali's ground troops in the battle for Konna.
BBC: Hollande steps up France security over Mali and Somalia
Mali's military has suffered heavy losses in previous clashes, including 11 soldiers killed and about 60 wounded in the battle for Konna, according to a government statement read on state TV.
French involvement began the day after militants said January 10 that they had seized the city of Konna, east of Diabaly in central Mali, and were poised to advance south toward Bamako.
The French pilot died while taking part Friday afternoon in an aerial operation targeting a terrorist group moving on the town of Mopti, near Konna, French Defense Minister Jean-Yves Le Drian said.
France's involvement in Mali began the day after militants said January 10 that they had seized the city of Konna, east of Diabaly in central Mali, and were poised to advance south toward Bamako.
The main allegations against the Malian military involve claims of killings in Sevare, in the centre of the country, after Islamist rebels captured the nearby town of Konna on 10 January, prompting the French intervention.
French involvement in the conflict began on January 11, the day after militants said they had seized the city of Konna, east of Diabaly in central Mali, and were poised to advance south toward Bamako.
Medical charity Medicins Sans Frontieres said it had received numerous reports of people being killed or injured in Konna, and that in Douentza, bombardments and fighting were preventing the wounded from making it to hospital.
French involvement in the conflict began on January 11, the day after militants said they had seized the city of Konna, east of Diabaly in central Mali, and were poised to advance south toward Bamako, the capital.
And when the militants last week advanced towards Konna, the northernmost outpost of government control, it seemed reasonable to speculate that the group's wily leader Iyad Ag Ghaly was merely stepping up the pressure in hope of securing extra concessions.
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