Eleven Malian soldiers who had been captured between July 2016 and March 2017 died in the raid on 23 October, according to military sources, confirmed by a Malian defence ministry official on Tuesday.
But the French general staff denies the claim, saying that the operation had targeted a "terrorist training camp" and that "at no moment" was the presence of Malian soldiers established.
The incident occurred near Abeibara, in the north-eastern Kidal region, during a raid on a group affiliated to al-Qaeda in the Islamic Maghreb.
The day after the attack the group concerned, Iyad Ag Ghali's GSIM, accused the French army of killing "11 Malian soldiers who were held captive ... and well as three mujahedin [fighters]".
It was not the first such accusation in Mali.
Minister meets ambassador, military representative
Mali's Defence Minister Tiéna Coulibaly met French ambassador Evelyne Decorps and a representative of France's military force in Mali on 31 October to discuss the incident.
Following that meeting, the commander of the French forces issued the denial, insisting that the operation "took out 15 terrorists, one of whom turned out to be a lieutenant".
Since the row has become public, a source has told the Reuters news agency that the soldiers were not prisoners but deserters who had joined the jihadists ranks, claiming that the Malian accusation was a "propaganda exercise" ahead of local and regional elections scheduled for 17 December.
MP demands investigation
Amadou Thiam, an MP from the Malian opposition ADP-Maliba party, called for the incident to be investigated.
"Eleven of our armed forces get killed by miscommunication or lack of communication. That is a disaster," he told RFI. "The [French] Barkhane forces are supposed to work in cooperation and in harmony with the armed forces of Mali. So it is quite unacceptable that 11 of our armed forces are captured somewhere, are taken hostage somewhere and the Barkhane forces are not aware of where they are.
"For us, it is too big of a mistake to be accepted. We think there should be an inquest, there's to be some investigation into how this happened."
France has a 4,000-strong force, called Barkhane, in northern Mali and is supporting a five-nation G5 Sahel force, designed to beef up security across the sprawling region south of the Sahara.