The fighting began at about 4am local time when "heavily armed men" attacked a base at Ngagara in the north of Bujumbura as well as a military training college in the south, according to the officer, who spoke to AFP on condition of anonymity.
"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.
Clashes continued throughout the morning in different parts of the capital.