The prison break was the second of its kind in recent weeks in Mali, where militant groups based in the desert north have extended their campaign into central and southern regions.
Five armed men attacked the jail at around 0115 GMT, injuring two guards, the Ministry of Security said.
Ninety prisoners remained at large on Tuesday afternoon after three were captured. The army was deployed in pursuit.
It was not immediately clear who was behind the attack, but a number of Islamist groups, some linked to al Qaeda, have stepped up their insurgency in Mali this year.
Army spokesman Diarran Kone said the attack bore the hallmarks of followers of radical Islamist preacher Amadou Koufa, the leader of an ethnic Fulani jihadist group, the Macina Liberation Front. It was unclear whether any suspected jihadists had been in the prison.
Last month, gunmen broke into a prison in southern Mali, freeing …