Clashes were reported at the national TV and radio station and at the garrison town near the capital Bamako that is the headquarters of the rebel soldiers led by Captain Amadou Haya Sanogo.
The resurgence of fighting dimmed hopes for a quick return to order in the west African country where the March 22 coup also allowed Tuareg rebels and Islamists to make large gains in the country's desert north.
The junta, under regional and international pressure, has allowed an interim government to take over but has kept making arrests, which witnesses said sparked the latest violence.
Fighting was reported at the national broadcaster, known as ORTM, a key target of the coup, as well as in Kati, the garrison town near Bamako that serves as the headquarters of the rebel soldiers.
The gunfights followed an attempt by junta loyalists to arrest a member of the presidential guard, or "Red Berets," witnesses said.
The US embassy reported the shooting on Twitter, writing: "Gunfire reported in ACI2000, vicinity of ORTM, and possibly other areas of #Bamako. U.S. Citizens advised to shelter in place."
An employee of the TV and radio station, which had been held by rebel soldiers since the coup, told AFP that "there were deaths" in the gunfight, without giving precise casualty figures.
Forces loyal to the junta were also attacked in Kati, although it was not clear by whom. "I am coming under fire," Samba Coulibaly, a member of the former junta, told AFP.
Another military source also said there had been shots fired and that civilians were leaving the town.
"Obviously, there is a coup against Sanogo" attempted by supporters of ousted president Toure, said a government source in a neighbouring country.
When the renegade soldiers staged their coup on March 22, shortly before scheduled elections, their power grab shattered the country's image as a democratic success story in the region.
Under diplomatic pressure from Mali's partners and military pressure from the advancing rebellion in the north of the country, the junta agreed to hand power over to Dioncounda Traore, the former parliament speaker.
Traore was sworn in as interim president on April 12, but the situation in the country has remained volatile.
In the north, an area the size of France is now in the hands of Tuareg separatist rebels, many of them battle-hardened and well-armed after serving as mercenaries in the Libyan conflict, and Islamist militias.
The regional grouping ECOWAS, the Economic Community of West African States, has mediated the handover to a civilian government and pressured the junta to return to the barracks, with mixed success.
The captain who led the coup, Sanogo, on Saturday rejected a decision by West African states to send troops to oversee the transition period, and their demand to have elections within 12 months.
A meeting that had been planned for Tuesday between an ECOWAS mediator, Burkina Faso President Blaise Compaore, and a delegation of the former junta was cancelled, a source close to the mediators said.
The delegation of rebels would not come because an aircraft in which they had been due to travel "could not land in Bamako," as gunfire was exchanged in the city late Monday, the source told AFP.
