At least 25 troops were killed after militants aboard heavily-armed vehicles raided two military camps at Boulkessy and Mondoro near the border with Burkina Faso, according to a provisional toll.
Fifteen jihadists were killed in the raids, according to government figures, which began early Monday and were quelled more than a day later.
About 60 Soldiers were listed as missing, according to a security source but late Wednesday the Malian army said 11 had returned to their base.
It is unknown whether the others have been killed or captured.
“Operations to secure the area are underway with Mali’s partners,” a Malian military source said.
“Our objective is to consolidate our presence in Boulkessy and to focus on soldiers of whom we are currently without news.”
President Ibrahim Boubacar Keita declared three days of national mourning would begin on Thursday, according to a government statement.
Hundreds of angry youths and wives of soldiers gathered outside a military camp in the capital Bamako late Wednesday to express their grievances.