The suspects were sentenced to jail terms ranging from three to 60 years, the ministry said.
"Most of them were convicted for professing to belong to the terrorist group, concealing information about the group which they knew or believe to be of material assistance that could lead to the arrest, prosecution or conviction of Boko Haram members," the justice ministry statement said.
Since last week, hundreds of suspected Boko Haram members have appeared before a court at the Kainji military base in Niger, a central Nigerian state.
It also freed 526 suspects, including minors, for lack of evidence and ordered they be sent to their state governments for "proper rehabilitation."
Seventy-three cases were adjourned for another hearing.
Among those released was a young girl from Nigeria's Borno State with a 3-month-old baby. She was arrested in 2014 while escaping Sambisa forest, a Boko Haram enclave.
The court on Friday imposed a second 15-year sentence on Haruna Yahaya, who was involved in the kidnapping of more than 200 schoolgirls from Chibok in 2014.