"A supply mission for the national armed forces fell into an ambush between Dogofri and Nampala. The initial toll is nine dead and five wounded," commerce minister and government spokesman Abdel Karim Konate said in a statement.
He condemned the "cowardly and barbaric act" and said "our commitment, as well as that of our partners, is to relentlessly pursue the fight against terrorism and drug trafficking" in Mali.
The troops' vehicle hit a mine and they were then ambushed by the group, a Malian security source told AFP, recounting what is a familiar jihadist tactic.
Nampala, a garrison town near the Mauritanian border, has been targeted by several jihadist attacks.
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Three Malian jihadist groups with previous Al-Qaeda links recently joined forces to create the "Group to Support Islam and Muslims" (GSIM), led by Iyad Ag Ghaly of Ansar Dine, and have also killed soldiers further east near the Burkina Faso border.
Barkhane's commander Francois-Xavier de Woillemont said in Ouagadougou the operation was not yet over, and the final goal of such missions was "to get rid of the terrorists" who "harass local people and stop them living a normal life."
It was the next step in operations undertaken in the zone "where we know that terrorists come to hide," he added.
Last July, 17 soldiers were killed in an attack on a military base in Nampala claimed by the Islamist organisation Ansar Dine.