The authorities first reported the attack in Indelimane, Menaka region, on Friday, but gave a lower provisional death toll.
"Heavily armed unidentified men attacked around noon. The attack started with shellfire.. Then they retreated toward Niger," government spokesman Yaya Sangare told Reuters on Saturday.
He added the death toll remained provisional as corpses were undergoing identification, and that the army was undertaking a combing operation on the ground with support from international forces, including French troops from the Barkhane operation and U.N. peacekeepers.
"The dispatched reinforcements found 54 bodies including one civilian, 10 survivors, and found considerable material damage," Sangare said on Twitter earlier on Saturday.
The attack follows jihadist raids in late September that underscored the increasing reach and sophistication of armed groups operating in the region.
From their stronghold in Mali, groups with al Qaeda and Islamic State links have been able to fan out across the Sahel, destabilizing parts of Niger and Burkina Faso.Thirty-eight Malian soldiers were killed on Sept. 30 in coordinated attacks on two army bases in central Mali, which has slipped from government control despite the presence of the French army and other international forces.