French troops have started to withdraw from Timbuktu after securing the fabled city as they ramped up their mission in another northern Mali city.
They are searching for Islamic extremists who may be mixing among the local population in Gao.
French military spokesman Colonel Thierry Burkhard said the operation to secure Gao is still under way, nearly two weeks after French and Malian troops moved into the area. New clashes nearby raised questions about how solid a hold the French military has on the strategic area.
There is a risk of "residual presence" of terrorists mixed among the population, Col Burkhard said from Paris. Extremists fired rocket launchers at French troops near Gao on Tuesday.
France launched a military operation in Mali on January 11 to help the Malian government restore control. Islamic extremists linked to al Qaida had imposed severe rule in northern Mali then started pushing toward the capital last month.
UN Secretary-General Ban Ki-moon said the military operation "so far has been effective and successful".
He said: "All these jihadists and armed groups and terrorist elements - seemingly - they have fled somewhere. Our concern is that they may come back. As you have seen yesterday, they are hitting back in some areas. It is good that Timbuktu and Gao and all these major cities have been cleared."
Soldiers in fatigues could be seen pushing an artillery cannon onto the barge crossing the Niger River, located on the southern perimeter of Timbuktu.
France has commandeered the river crossing, and small convoys of military vehicles were lining up, waiting for the barge, including armoured cars, trucks, and vehicles loaded with supplies, including crates of bottled water.
While the population of Timbuktu is anxious, worrying that the departure of French troops will open the door for the Islamists to return, French military officials said they had fulfilled their mission. French president Francois Hollande has said France could begin withdrawing its 4,000 troops from Mali as early as March.