The cause of the fire was not immediately known and as yet there has been no official comment on the incident.
The fire broke out at the prison facility in Gitega at about 4:00 am (0200 GMT) and destroyed several areas of the prison.
The prison housed more than 1,500 inmates at the end of November, according to prison authority figures, far higher than its capacity of 400.
Emergency services allegedly came late to the scene, with a water trucks arriving only two hours after the start of the blaze
In August, the prison was also struck by another fire without causing any casualties, according to the interior ministry, which blamed it on an electrical short-circuit.
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