Witnesses said that they saw dozens of dead bodies, the total number rising to nearly 90, on the streets of Burundi’s capital, on Saturday; a day after anti-government gunmen attacked two military bases and a military college.
Army spokesman Gaspard Baratuza said 79 attackers were killed while 45 others were arrested.
There were four policemen and four soldiers among the deceased.
"Sweep operations have finished now," Baratuza said, adding that officials confiscated weapons and ammunition.
Clashes escalated on the streets of capital Bujumbura after unidentified gunmen attacked three military bases.
Witnesses have claimed that police officers carried out extrajudicial killings, as they broke down doors while searching for people and shooting them.
A senior police official told Reuters that there were 20 young men killed in the neighbourhood.
One witness described some of the victims as "kids" and said they had been shot execution style "through the top of the skull."
"It is an absolute horror, those who committed this are war criminals," the witness told AFP.
"Most of those killed are young heads of households who were at home... its carnage, there is no other word for it," a resident of Nyakabiga said.
"They entered in our compounds, gathered all young and middle aged men, took them and killed them away from their homes," another resident told Reuters.
But police spokesman Pierre Nkurikiye said there were "no collateral victims."
"All the deaths were attackers killed in the joint sweep operation of the army and police," he said.
"The enemy was neutralised."
In Musaga, which is close to the military college that was attacked on Friday, a witness said "I have counted 14 dead bodies with my own eyes," blaming "soldiers and police" for the killings.
Rwanda and Ethiopia airlines have cancelled their flights following the events that took place on Friday, but Kenya announced it will resume the scheduled flights.
Kenya Airways Resumes Day Flights to Bujumbura: https://t.co/ZnNeo3JGgC
— Kenya Airways (@KenyaAirways) December 12, 2015
The country has been rocked with a cycle of violence since President Pierre Nkurunziza announced his bid for third term in April, despite a two term limit in the constitution.
The United Nations has warned on Tuesday that there is a risk of civil war in Burundi, if deadly violence is not stopped.
Attacks overnight in Bujumbura risk destabilizing already volatile situation–we strongly condemn & urge immediate political dialogue
— Samantha Power (@AmbassadorPower) December 11, 2015
Burundi suffered a civil war between 1993 to 2005 and some 300,000 people died in the conflict between rebels from the country's majority Hutu population and an army dominated by the Tutsi minority.
At least 250 people have died in the latest violence and more than 210,000 people have fled to neighbouring countries.