Former Tuareg rebels are reported have left two military bases which they had been occupying in north-eastern Mali.
Diplomatic sources told the BBC the situation remained tense in the remote region, following two separate raids on the towns of Kidal and Menaka.
President Amadou Toumani Toure appealed to Malians to stay calm and not confuse the attackers with ordinary Tuaregs.
This follows race riots in Mali during the Tuareg rebellion, which ended when a peace deal was signed in 1998.
Eyewitnesses say the rebels left in trucks mounted with machine guns. They describe petrified women and children fleeing from nearby villages fearing for their lives.
Following the peace deal, many former Tuareg rebels were integrated into the army but some have since deserted.
Malian military officials say these deserters are behind the attack on Kidal.
"I have seen the bodies of two dead soldiers and four seriously wounded whom we can't get to hospital because the town is still occupied," Kidal's police commissioner, Mady Fofana, told Reuters news agency.
Amy reinforcements are reported to be on their way to Kidal from Gao, 300km to the south.
A journalist in Menaka - also on one of the main roads north from Mali, across the Sahara desert - said that deserters there had plundered the city's barracks, stealing weapons.
Mohamed Raba told the AP news agency there had been "great panic" in the town.
It is not yet clear whether the attacks mark the start of a new rebellion or are simply a criminal act.
Banditry is common around Kidal, which is the gateway to the Sahara desert and on a route used to smuggle migrants and contraband goods.
The rumoured discovery of oil reserves has also focused attention on the region.
The United States has been training Mali's army in counter-insurgency, fearing that Islamic radicals could spread south from Algeria.