An army spokesman says 87 people were confirmed dead after insurgents attacked three military barracks. Many were killed in an apparent retaliation, when the military fired on opposition neighborhoods.
Security forces in Burundi have been accused of extrajudicial killings after a series of coordinated attacks on military bases around the capital Bujumbura.
The country's military confirmed that almost 90 people had been killed in the assaults, which took place on Friday, and in the violent aftermath.
Local residents say they awoke on Saturday to find 39 dead bodies lying in the streets of the city. Several witnesses have accused soldiers and police of breaking down doors to homes, dragging out young men and executing them.
"The final toll of the attacks yesterday is 79 enemies killed, 45 captured and 97 weapons seized, and on our side eight soldiers and policemen were killed and 21 wounded," said military spokesman Colonel Gaspard Baratuza on Saturday.
After Friday's attacks, "fighting continued into the night and the corpses found in these neighborhoods this morning are enemies," Baratuza added.
Some residents accused authorities of trying to hide evidence of a massacre by the security forces in an apparent retaliation for the attacks.
"Most of those killed are young heads of households who were at home... it's carnage, there is no other word for it," one outraged resident of Nyakabiga told Agence-France Presse.
Some of the victims had their arms tied behind their backs while others were killed at close range, according to witnesses.
President's opponents targeted
Anschaire Nikoyagize, the president of the Burundian League for Human Rights, told the DPA news agency that many of those killed had been detained in prisons for protesting against President Pierre Nkurunziza.
A European diplomat in Bujumbura claimed the government was seeking to downplay the extent of the killings. "There are dozens of bodies in other protest districts, such as Mutakura and Cibitoke, but the authorities are trying to make them disappear," the diplomat said.
Friday's attacks saw heavily-armed gunmen launched coordinated assaults on the at the Ngagara base and a military training college in the capital, as well as on a military base in Mujejuru, 40 kilometers (25 miles) away. just before 4 a.m. local time.
Officials said military equipment and large quantities of ammunition had been seized. The stolen items were later recovered by the military.
Earlier, DW correspondent Apollinaire Niyirora said the army had appeared to be prepared for some kind of incident as tension had noticeably increased in Bujumbura the day before Friday's attacks. He predicted that the government would use the violence as a pretext to clamp down on the opposition.
This week's attacks were the worst violence since a failed coup attempt in May, sparked by President Pierre Nkurunziza's bid for a third term in office which he won in July.
Hundreds of people have been killed in protests, armed attacks and assassinations since the unrest began in April and more than 200,000 have left the country, according to UN figures.
mm/jm (AFP, AP, dpa)