The clash erupted at a base housing paratroopers loyal to ex-president Amadou Toumani Toure, who was ousted in a March 2012 coup.
The paratroopers were protesting an order absorbing them into other units to be sent to the frontline. Their demonstration devolved into a firefight with rival troops that killed two adolescents and wounded another 13 people, according to state media.
Interim president Dioncounda Traore reprimanded the military over the incident.
He said his prime minister, Diango Cissoko, would meet with paratroopers Monday to “find a lasting solution to this crisis”.
The fighting overshadowed the arrival of 70 EU military trainers, the first of what is to be a 500-strong mission tasked with whipping the Malian army into shape.
French General Francois Lecointre, leading the mission, said there was “a real need to rebuild the Malian army, which is in a state of advanced disrepair”.
The nation imploded last year after the coup, waged by soldiers who blamed the government for the army’s humiliation by a rebellion among the Tuareg, a North African people who have long complained of being marginalised by the south.
A month later, paratroopers launched a failed counter-coup that left 20 people dead.
With Bamako in disarray, Al-Qaeda-linked fighters hijacked the Tuareg rebellion and took control of the north, imposing a brutal form of Islamic law.
French special forces and Chadian troops on Friday secured the strategic oasis of Tessalit, near the Algerian border in the far northeast, and sought to flush the Islamists out of hiding in the Adrar des Ifoghas mountains, where they are believed to have fled with seven French hostages.
US State Department spokeswoman Victoria Nuland urged countries not to pay ransoms to free their hostages, after a former US ambassador to Mali estimated that Western countries had paid as much as $89 million (66.6 million euros) from 2004 to 2011 in ransom payments to the militants French troops are now fighting.
Paying ransoms is “just feeding into the coffers of the terrorists”, Nuland said.
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