Malian soldiers clashed with stone-throwing protesters who blocked a visit by the prime minister to the northern rebel stronghold of Kidal on Thursday.
Several demonstrators were wounded but there were conflicting accounts of who was to blame.
The west African country is in the process of restoring democracy after a coup last year led to al Qaeda-linked Islamists taking control of the north.
A French-led military offensive routed the Islamists, but tension remains between the central government and Tuareg separatists demanding an independent homeland they call Azawad. The two sides are due to open negotiations over the status of the restive desert region.
Pro-independence protesters marched to the airport in Kidal, which is home to the MNLA separatist rebel group, in the late morning ahead of the planned arrival of Prime Minister Oumar Tatam Ly.
“The demonstrators at the airport attacked the soldiers who were there to welcome the prime minister, first by throwing projectiles and then with hidden gunmen,” Interior Minister Sada Samake said on state television.
He said soldiers responded by firing into the air to disperse the crowds. While he said three protesters were wounded, he blamed the injuries on gunfire from snipers.
The prime minister’s visit was cancelled.
Kidal residents also said the army had fired shots during the confrontation and that three people had been injured. However they could not confirm the government’s claim that hidden gunmen were involved in the clashes.
The MNLA said United Nations peacekeepers and French soldiers were also present during the confrontation. It accused Malian soldiers of firing into the crowd and said seven demonstrators were wounded, including four women.
“This episode demonstrates once again the serious violations of the rights of the civilian population of Azawad, and that of Kidal in particular, by the Malian army since its return to these territories,” the rebels said in a statement.
The French military operation in Mali, known as Serval, and the United Nations’ MINUSMA peacekeeping mission both declined to comment on the incident.
The MNLA seized control of Kidal after France’s military intervention in January smashed a loose coalition of Islamist militants that had over-run northern Mali last year.
The MNLA were initially allied with the Islamists against the government. However, they were later sidelined by the better armed Islamists and were not targeted by the French.
Mali’s interim government signed a peace agreement with Tuareg representatives in Ouagadougou, the capital of Burkina Faso, in mid-June, allowing national elections to take place. As part of the deal, Bamako agreed to open talks over the Tuaregs demands for more autonomy.