"French soldiers of the Barkhane military operation were ambushed by terrorists" near the town of Bourem, a Western military source told the AFP news agency.
Earlier the ministry said the dead were French soldiers but it later changed its story.
It told news agencies that four to eight French soldiers were injured.
Eyewitnesses say that the soldiers' armoured car was blocked by a vehicle driven by a suicide bomber who blew it up.
The Malian defence ministry confirmed the incident, which came two days after a deadly attack on the headquarters of the five-nation G5 Sahel African force, in the country.
An African Union summit opened in Mauritania's capital, Nouakchott, on Sunday.
French President Emmanuel Macron is to meet leaders of the countries participating in the G5 force - Mauritania, Mali, Burkina Faso, Niger and Chad - during the summit.
France, which intervened in Mali in January 2013 after the north fell to Islamists and Tuareg separatists, hopes that the G5 will take over the battle against armed jihadists and smugglers in the desert region.