The Tuaregs stormed two bases near the Sahara desert town of Kidal. The former rebel chief of a base at Menaka, close to the Niger border, then "looted his own camp's weapons depot" before attacking a nearby national guard base, army sources said.
Gunfire was reported but there were no confirmed reports of casualties.
Soldiers and civilians said that most of the 400 or so troops at Kidal fled during the early morning incidents, when the Tuaregs raced to the assault on four-wheel-drive vehicles.
Military sources said the attackers were renegade members of a Tuareg group that was active in the first half of the 1990s before being integrated into the west African country's army ranks under a peace deal.
The Tauregs have for centuries been a main nomadic desert people who live across borders.
President Amadou Toumani Toure went on state radio to pledge that the government would "manage the situation with responsibility but also with balance," noting that Malians face tough economic and social challenges.
"Armed units have attacked the essential military bases we have at Kidal. This is harmful, but in the face of challenges ... I ask every Malian to stay calm, safe and show a level head whatever the situation," Mr Toure added.
The former Tuareg rebel leader at Menaka, who had several hundred men at his command and integrated into army ranks under peace deals, was named as Major Bah Moussa by a military source.
One resident living near the national guard camp said several people were injured in light arms fire, but military authorities confirmed no details of casualties in what appeared to be a concerted series of attacks.
The incident at Menaka was reported after the lightning raids in the Kidal region, 365 kilometres (225 miles) to the south. The gunfire seemed mainly to have been a scare tactic.
Scores of armed men who were later identified as members of the Tuareg community swooped on the Aboulaye Soumare camp, one of two, at around 6am local time.
An officer who witnessed the attack said dozens of Malian soldiers were in the camp near Kidal town at the time, and that around 20 were still being held captive afterwards.
He reported small-arms fire "before, during and after" the seizure of the base.
Local residents said "turbaned" men seized a second camp southeast of Kidal two hours later. In both cases they looted the armouries.
Without giving details, President Toure said "those who attacked should not be confused with other Tamasheq (Tuaregs) who live with us. ... In Mali, you don't have to take up arms to make your point."
He added that he had no plans to rush home to Bamako from his current tour and was speaking from Kayes in the southwest.
In Mali, many rebels joined the army under a social and military integration plan but some deserted, dissatisfied with terms offered by a government keen to see people who have long shown little regard for national borders become full citizens of the post-independence states of the region.
Cases of unrest are sporadic. One renegade senior officer quit the ranks in February and then returned in March.
The Malian army has been receiving military training from the United States, which is concerned that the vast areas in the Sahara straddling several borders serve as bases and training areas for armed Islamic extremist movements.
They also serve as routes for contraband smugglers and Africans heading north in hopes of immigrating to Europe and a better life.