In a letter to the head of the United Nations Security Council dated Monday, Mali's foreign affairs minister, Abdoulaye Diop, said its airspace has been breached more than 50 times this year, mostly by French forces using drones, military helicopters and fighter jets.
"These flagrant violations of Malian airspace were used by France to collect information for terrorist groups operating in the Sahel and to drop arms and ammunition to them," the letter said.
Mali provided no evidence to back its accusations.
France has spent a decade and billions of dollars to stamp out Islamist militants, some with links to al-Qaeda and Islamic State, in its former colony.
"France has obviously never supported, directly or indirectly, these terrorist groups, which remain its designated enemies across the planet," said the French Embassy in Mali in a Twitter thread.
It said that 53 French soldiers had died during its nine-year mission in Mali and that France had killed hundreds of Islamist fighters in order to improve security for Malians. France has also suffered Islamist attacks at home, it added.
France this week pulled the last of its troops out of Mali as Russian mercenaries hired by Mali's military government expand their reach. The swap worries western powers who see their influence slipping in the Sahel.
Russian President Vladimir Putin discussed possibly supplying food, fertilizers and fuel to Mali in a call with the country's interim president last week.
German U.N. soldiers said they saw Russian forces landing at the airport and unloading equipment on Monday in the northern town of Gao, the day the last French soldiers left.
French forces were welcomed as heroes in Mali in 2013 when they beat back Islamist groups that had taken over the north, including the fabled city of Timbuktu.
But a series of setbacks and prolonged attacks by the militants have soured relations, which became worse since a military junta overthrew the government in 2020 and later overthrew an interim civilian cabinet.