A court at a military base in Kainji, in the central state of Niger, was told yesterday that 1,669 suspects were awaiting trial at the facility. Of those, 1,631 were men, 11 were women, with 26 boys and one girl.
All of the defendants have been arrested and detained since the start of Boko Haram's Islamist insurgency in 2009, which has left at least 20,000 dead and forced more than 2.6 million others from their homes.
The ministry has said 651 others held at the Giwa barracks in the capital of the northeastern state of Borno, Maiduguri, would then be tried.
Isah said in a statement that Judge Binta Nyako began proceedings at 1:35 pm (1235 GMT) after touring the courts with three other judges, state prosecutors and Legal Aid Council defence lawyers.
"We are here to ensure that nobody is persecuted. We are here for prosecution and so we have come with open minds," she was quoted as saying.