Interior Ministry officials said the majority of the victims of the latest fighting were rebels and civilians.
Though no official figure was available yet on the casualties suffered by the government forces, military officials estimated that as many as 30 soldiers could have died in the fighting.
The intense fighting broke out last Monday when rebels of the National Liberation Forces (FNL) attacked southern areas of the capital.
Officials said the highly decomposed state of the victims' bodies was making it difficult to ascertain whether they were civilians or rebels.
Fighting has been continuing for five days with the FNL rebels launching intermittent rocket attacks on the city centre.
But the Tutsi-dominated Burundi army said the rebel attacks had been repulsed and the FNL fighters were forced to retreat as far back as 10 kilometers from the capital.
Rated as the world’s third least developed country, Burundi has been wrecked by a continuous civil war with Hutus fighting to end the political dominance of the minority Tutsis.
The continuing conflict, often fuelled by interference of neighbouring countries, has so far claimed more than 300,000 lives.