The violence compounds an already dire security situation in the desert region used by armed groups to launch attacks in Mali and neighbouring countries in West and Central Africa.
The identity of the assailants was unknown, but disputes between the nomadic Tuareg and herder Fulani ethnic groups have killed several hundred and displaced thousands this year.
Menaka town mayor Nanout Kotia told Reuters news agency that 43 Tuareg died in a village 20km from the town over the past two days.
“Armed men riding motorbikes attacked several nomadic campsites in Tinabaw. They shot indiscriminately at the population,” Kotia told Reuters, saying security forces had been sent to the area.
Mali’s main Tuareg separatist group, the Coordination of Azawad Movements, said 47 Tuareg civilians were killed in the Tinabaw area. Nobody has claimed responsibility.
Armed men killed 15 Fulani civilians in Mali’s central Mopti region earlier this month.
Mali has been in turmoil since Tuareg rebels and loosely allied armed fighters took over its north in 2012, prompting French forces to intervene to push them back the following year.
They have since regained a foothold in the north and centre, tapping into ethnic rivalries to recruit new members.