It was just the latest in a series of violent incidents at prisons in the troubled country.
Philemon Yogolelo told reporters that so far there had been one confirmed death, four seriously wounded and that about 20 prisoners had escaped. He was speaking after visiting the prison an hour after the incident.
Two Burundian soldiers in detention had thrown a grenade that had destroyed an entrance to the prison, permitting the break-out, said army spokesman Captain Dieudonne Kasereka.
Bukavu is the regional capital of South Kivu province and lies on the border with Rwanda.
The incident is just the latest in a series of outbreaks of violence at prisons in the country.
On May 17, more than 4,000 prisoners escaped from Kamama prison in the capital Kinshasa, again after an armed assault.
On June 11, at Beni, in the neighbouring province of North Kivu, more than 900 prisoners escaped after an attack by an unidentified force, said officials.
The country is struggling with a political crisis, with President Joseph Kabila still in power despite his mandate having ended on December 20 last year and no date set for promised elections.
The east of the country in particular has for more than 20 years been prey to attacks by rival armed groups.
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