The attacks on Monday evening on the villages of Yoro and Gangafani 2 compound a dire security situation in central Mali, where ethnic militias regularly slaughter civilians from rival groups and Islamist militants are also active.
The victims of Monday's raids were mostly ethnic Dogons, said Issiaka Ganame, the mayor of Yoro, where 24 people were killed. Another 17 died in Gangafani 2.
"About 100 unidentified armed men circulating on motos all of a sudden invaded Yoro and fired on the population," Ganame told Reuters. "Then they descended on the village of Gangafani 2, which is about 15 km (9 miles) away."
The tit-for-tat violence in recent months has largely pitted Dogon hunters against Fulani herders. Attackers believed to be Fulani raided a Dogon village last week, killing at least 35 people.
In March, suspected Dogon militiamen killed more than 150 Fulani in two villages in central Mali, one of the worst acts of bloodshed in the country's recent history.
President Ibrahim Boubacar Keita's government has vowed to disarm the militias but has struggled to do so. The groups are looked to for security by local communities who do not trust the government to protect them.
On Tuesday, two labor unions representing civil servants called on state adminstrators in the Mopti region, where most of the attacks have occurred, to leave their posts and decamp to the regional capital due to death threats.
"President Keita said he was going to disarm all the militias. We take note and await the disarmament of the militias and implementation of protection measures," said Ousmane Christian Diarra, secretary-general of the National Syndicate of Civil Administrators.French forces intervened in Mali, a former French colony, in 2013 to push back a jihadist advance from the north. But the militants have since regrouped and use northern and central Mali as launchpads to stage attacks across the region and stoke tensions among different communities.