Witnesses described how violence erupted as a huge crowd of angry youths, gathering for a second day outside the MINUSMA headquarters in the city of Gao, threw stones and attempted to storm the building.
"Here in the morgue in Gao we have at least three dead protesters, some killed by gunshot wounds... There are also several serious injuries," a hospital official told AFP.
An official in the ministry for security and civil protection confirmed the deaths, adding that the situation remained "very tense".
"We are in very close contact with the Malian authorities," he added.
An independent source contacted by AFP described how youths had climbed onto MINUSMA vehicles while others threw petrol bombs at MINUSMA soldiers.
"It was on the verge of a riot. It's very tense, I heard gunshots," the source said.