The Coordination of Azawad Movements (CMA) said in a Facebook post that their forces "repulsed a complex attack by the Fama (Malian army) and Wagner" in the town of Ber, in the northern Timbuktu region.
"We call the international community to witness these serious acts," said CMA spokesman Mohamed Elmaouloud Ramadane, denouncing the attack as a "violation of all security commitments and arrangements".
Mali's army said it had "vigorously retaliated" against an "attempted incursion" into their position on Friday, blaming "terrorists" for the incident.
On Thursday, the Tuareg former rebels announced the departure of all their representatives from Bamako for "security" reasons, further widening the gap with the junta, which has been in power since 2020.
The CMA is an alliance of Tuareg-dominated groups seeking autonomy or independence from the Malian state.
It is one of the parties to a 2015 peace agreement with the Malian government.
Mali's military government has fallen out with former colonial power France and turned to Russia for political and military support.
Wagner is openly active in Mali and at least three other African countries, typically shoring up fragile regimes in exchange for minerals and other natural wealth.
In Mali, Wagner paramilitaries protect the regime, conduct military operations and training, and advise on the revision of mining laws and even the constitution.
The regime in Bamako says the foreign military instructors in Mali are not from Wagner but from the regular Russian army.
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