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Bodies litter the streets of the capital Bujumbura in the worst outbreak of violence in the troubled east African country for months.
One eyewitness said he counted 21 bodies with bullet wounds in their heads in the Nyakabiga neighbourhood on Saturday morning.
Some of the victims appeared to have had their hands tied behind their backs.
Residents have claimed that security forces loyal to President Pierre Nkurunziza have been searching houses, dragging people away and shooting them, some with their hands tied.
The sound of gunfire could be heard throughout Friday and overnight in the city. Residents hid in fear, with only soldiers and police patrolling the streets.
Burundi has been in crisis since Mr Nkurunziza was re-elected for a third term in July after an aborted coup. His opponents said it was illegal for him to stand for a third time.
Colonel Gaspard Baratuza of the Burundian army said co-ordinated attacks on three military installations had left 87 people dead.
He said more than 150 armed men raided army facilities on Friday and 79 were killed.
Eight security agents – four from the army and four from police – also died in the fighting, while 21 security officers were wounded.
Col Baratuza said government forces arrested 45 members of the unidentified group that attacked the installations.
It is not clear if the death toll includes the bodies found in Bujumbura, some of which were filmed by news agencies.