The troops "repelled a terrorist attack in the early morning," in the central town of Boni," the ministry said.
The army forces "killed 13 terrorists and recovered arms and munitions," and three soldiers were killed while the attack was repelled, the statement added.
Earlier, military sources told AFP that two troops had been killed, along with 13 terrorists in two attacks in the region.
Residents in Boni told AFP that helicopters were later circling the area but that calm had returned by afternoon.
In June 2015, Mali's government signed a peace agreement with coalitions of armed groups. But the jihadists remain active, and large tracts of the country remain lawless.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)