- Boko Haram insurgency has left 20,000 dead and forced more than 2.6 million to flee from their homes.
The Justice ministry promised to prosecute and not to persecute the suspects.
Many of the detainees have been held at military detention facilities for years without access to a lawyer or ever having appeared before a judge.
Nigeria began its first major trials of Boko Haram suspects on Monday, with a promise to "prosecute and not to persecute" defendants at the closed-door hearings, the Justice ministry said.
A court at a military base in Kainji, in the central state of Niger, was told 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 media has been barred from covering the cases on security grounds.
Justice ministry spokesman Salihu Othman Isah said the cases would be heard at four courts at the Kainji facility.
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.
"We (the judges) have been assigned to these cases and we have no other jobs for now."
Nyako, who normally sits at the Federal High Court in Abuja, criticised the government for failing to invite Nigeria's human rights watchdog to monitor proceedings, according to Isah.
The judge said the settings — civilian courts in a military base — were not ideal but added: "We shall make do with what we have.
"I think the (Federal) Ministry of Justice should have invited the National Human Rights Commission to witness the proceedings here. I hope it will do so in subsequent ones."
Nkiruka Jones Nebo, from the public prosecutor's office, said the military had kept the detainees "in good condition" and promised that the trials would "be seen to be just and fair", the justice ministry statement said.