This image taken from a video shows soldiers burying bodies near an army base in northern Mali. AP
The drone "illegally" flew over the Gossi base on April 20, the day after French forces handed the site back to Mali, the junta said in a statement.
The following day, the French army shared a video it said showed Russian mercenaries covering bodies with sand to falsely accuse the departing troops of war crimes. Two soldiers could be seen filming the half-buried corpses.
Earlier on Tuesday, Mali's military announced an inquiry into the discovery of a mass grave at the Gossi base.
The army said it found the grave the day after the images were published, and claimed the bodies' advanced stage of putrefaction ruled out Malian soldiers' responsibility.
It subsequently accused France of spying and attempting to sully the reputation of Malian forces with the drone-filmed video.
"The said drone was present... to spy on our brave FAMa (Malian armed forces)," government spokesman Abdoulaye Maiga said.
"In addition to the spying, French forces were guilty of subversion by publishing false images worked up to accuse the FAMa of responsibility for killing civilians, with the aim of tarnishing their image."
Bamako said "foreign aircraft, notably operated by French forces" had deliberately violated Malian airspace more than 50 times since the start of the year.
France, Mali's former colonial power, is winding down its almost decade-long, anti-jihadist military operation in the West African state.
But in February, it decided to pull out its troops after falling out with the military junta, especially over its rapprochement with the Kremlin.
France and the United States have accused mercenaries from the Kremlin-linked security firm Wagner of deploying in Mali, where the junta claims the Russians are just military instructors helping to restore order.
Vast swathes of Mali lie beyond government control due to the jihadist insurgency, which began in 2012 before spreading three years later to neighbouring Burkina Faso and Niger.
The impoverished and landlocked Sahel state has been ruled by a military junta since an August 2020 coup, which was propelled by protests against the government's handling of the war against the jihadists.
The conflict was said to have led to thousands of military and civilian deaths and forced hundreds of thousands of people to flee their homes.
The junta initially promised to restore civilian rule, but it failed to meet an earlier commitment to West African bloc ECOWAS to hold elections in February this year, prompting regional sanctions.