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 militants, according to government figures, were killed in the raids, which began early Monday and were only quelled on Tuesday, Presstv Reported.
But around 60 soldiers are listed as missing -- 78, according to a security source -- with no details as to whether they have been killed or captured.
"Operations to secure the area are under way 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."
The losses are a crushing blow to Mali's armed forces, which are flailing in the face of a militant revolt that has spread from the arid north to its center, an ethnically mixed and volatile region.
The operation is also a humiliation for the so-called G5 Sahel force -- a much-trumpeted initiative under which five countries decided to create a joint 5,000-man anti-terror force -- and for France, which is committed to shoring up the fragile region.
The losses symbolise "the escalating activities of violent extremist groups (in the Sahel) with more and more ambitious targets," said Baba Dakono of the Institute for Security Studies (ISS), a think tank based in Senegal.
Boulkessy is located in a gateway position in the center of the country, controlling access from Mali to parts of Niger and Burkina Faso -- countries that are also heavily targeted by militants.
Armed groups "have no interest in letting a military force (in Boulkessy) consolidate its position," said Dakono.
Only 13 soldiers emerged unscathed from the attacks, which were eventually subdued with the help of Malian special forces and foreign allies, including French warplanes.
The militants also made off with a large quantity of arms, ammunition and equipment -- local media say about 20 vehicles were captured, including some mounted with machine-guns.
According to an army report seen by AFP, two army helicopters and about a dozen vehicles were burned in the attack on Boulkessy.
The camp there -- which housed a Malian battalion that was part of the G5 Sahel -- was destroyed.
The G5 Sahel secretariat said the assailants were members of Ansarul Islam, a militant group accused of multiple attacks in northern Burkina Faso. Other sources were unable to confirm this.
Militants lost control of northern Mali after French military intervention, but regrouped to carry out hit-and-run raids and road mine attacks -- classic tactics by a mobile guerrilla force.
They have also moved on to the country's central region, where they have inflamed long-standing resentments between ethnic groups, analysts say.
On March 17, the Malian army lost nearly 30 men in an attack on a camp in Dioura, also in the troubled central region.
That assault came on the heels of a massacre of 160 Fulani (also called Peul) villagers -- a bloodbath that led to a military reshuffle and the government's resignation.
UN chief Antonio Guterres has been pounding the drum for help for Sahel states, among the poorest in the world, in their struggle against the mobile, well-armed and ruthless militants.
"We are losing ground to violence and terrorism," he said last week at a meeting on Mali and the Sahel, adding that the number of civilian deaths in the region had quadrupled between 2012 and 2018.
"The situation in the Sahel has become a regional threat," Guterres added, calling for an urgent increase in support.
On September 14, the West African regional group ECOWAS announced a billion-dollar plan to help fund the military operations of the nations involved. Full details will be presented at a summit in December.