Fighting began at around 4:00 am (0600 GMT) when "heavily armed men" attacked a base at Ngagara in the north of the city and a military training college in the south, according to a senior military officer.
"After more than two hours of clashes, the army repulsed the southern attack, while virtually all the attackers were killed in Ngagara base," the officer said.
"There are dozens of deaths among the attackers, and we also have losses," he said, adding the situation would soon be brought "completely" under control.
The fighting is the heaviest since a failed coup in May, sparked by President Pierre Nkurunziza's bid for a third term which he later won in disputed elections in July.
"I am holed up in the corridor of my house with my wife and children," said Eric, a resident of Musaga. "Pray for us because we will die!"
A government spokesman confirmed the attacks on Twitter, referring to the gunmen as "Sindumuja", meaning "I am not a slave", a name sometimes used for the insurgents.
Pacific Nininahazwe, an exiled civil society activist and anti-Nkurunziza protest leader said that, "at least two camps were attacked" and weapons looted and claimed that "soldiers have joined the rebels".
Exchanges of fire could still be heard in several neighbourhoods of Bujumbura by 8:30 early today, when most people would be heading to work. Instead, the streets were empty as city residents stayed home.
"All bridges are under army control and no movement is being permitted from one area to another," the senior military officer told AFP.
"This is a very worrying escalation because it is genuine military, or paramilitary, operations taking place in the capital," said one European diplomat.
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