The military camps came under attack on Monday at Boulkessy and Mondoro, towns near the border with Burkina Faso, and intense fighting continued on Tuesday with Malian troops backed by air support, sources said.
The Malian army regained control of the attacked positions in Boulkessy and Mondoro, said the government, but much equipment was lost.
It added that 15 jihadist fighters were killed in the assaults.
The assailants at Boulkessy are "suspected members of Ansarul Islam", the G5 Sahel said Monday.
The G5 Sahel is a five-nation joint taskforce created in 2014 to try to tackle jihadist violence in the region.
A local official previously told AFP that two civilians were shot dead in Boulkessy.
A military source said that a large deployment of resources was made after Boulkessy had "fallen into the hands of terrorists".
A local official in a nearby town earlier confirmed that he saw a Malian army helicopter headed towards Boulkessy.
Northern Mali fell into the hands of jihadists in 2012 before the militants were forced out by a French-led military intervention.
But much of the region remains chronically unstable and jihadist-led violence has spread to the centre of the country, often sparking bloodshed between ethnic groups.
Neighbouring Burkina Faso and Niger have also been infiltrated by insurgents, at the cost of hundreds of lives.
Ansarul Islam has been accused of numerous attacks in Burkina Faso since emerging in the border region in 2016.
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