Witnesses claim the incident, that took place in the town of Boulekessi near Mali's border with Burkina Faso, was due to military "blunders" and that "more than 15 civilians were killed," according to a former Malian minister.
At least 12 civilians were killed in northern Mali in an attack on a market that also involved the shooting of a Malian soldier, military sources said on Sunday.
The attack took place Saturday in the town of Boulekessi near the border with Burkina Faso.
"Malian troops under the G5 Sahel command are at the centre of this incident," a military source from the joint force of soldiers from five Sahel countries told AFP.
"One of the soldiers had been attacked by an armed man at the market in Boulekessi. Afterwards, in circumstances not yet clear, at least 12 civilians at the site were killed," the source said.
A Malian military source added that it was difficult to contact the region by phone and that an investigation was under way "to find out exactly how many civilians were killed and who shot the soldier."
Contacted by AFP, a former Malian minister, who comes from the region, said that witnesses had claimed the incident was due to military "blunders" and that "more than 15 civilians were killed".
"According to two witnesses, an armed man shot a Malian soldier who was now fighting for his life," the ex-minister said, adding that he was waiting for confirmation of the details of the incident.
Mali's defence minister Tienan Coulibaly could not been reached for comment.
The Malian army is often accused of making arbitrary arrests and carrying out extra-judicial executions in its fight against militants in the north of the country.
France intervened militarily in Mali in 2013 to help government forces drive Al Qaeda-linked militants out of the north.
But large tracts of the country remain lawless despite a peace accord signed with ethnic Tuareg leaders in mid-2015 aimed at isolating the militants.
The violence has also spilled over into both Burkina Faso and Niger.