"The army was able to catch some and is launching a pursuit," the Reuters news agency quotes Defence Ministry spokesman Abdoulaye Sidibe as saying.
Malian officials and local media believe that Islamist militants were behind the prison break
It is unclear whether there were any jihadists at the prison at the time.
Last month, gunmen broke into another prison, in Banamba in southern Mali, with the aim of releasing some inmates who had already been moved, the authorities said.
Several Islamist armed groups operate in Mali's northern deserts.
UN peacekeepers have been based in the country following an intervention by the French military in 2013 to oust the Islamist militants from northern towns.