The first major prosecutions of people arrested during the insurgency began last October, involving 1,669 suspects held at the facility in Kainji, Niger state.
The justice ministry has said 468 were released after it was found they had no case to answer; 45 were sentenced to between two and 15 years in jail; and 28 had their cases transferred.
A further 82 pleaded guilty in exchange for a lesser prison sentence or release taking into account time served in custody.
The remainder have had their cases adjourned pending further investigations.
Nigeria’s government banned the media and public from attending the trials, leading to criticism from the UN and human rights groups.
But the justice ministry said the second phase of proceedings would now be open to some civil society groups, including human rights organisations and the media.
Nigeria’s military has been accused of arbitrarily arresting civilians and holding them for years on end without access to lawyers.
Conditions have been described as overcrowded and unsanitary, while detainees have allegedly been tortured, died from illness or disease or were summarily executed.
Nearly nine years of conflict have left at least 20,000 dead and forced 2.6 million others from their homes, triggering a humanitarian crisis across the region.