In 2009 jihadist group Boko Haram launched an insurgency seeking to overthrow the government and establish an Islamic state.
The insurgency has killed tens of thousands and forced more than 2 million people to flee their homes, spawning one of the world's worst humanitarian crises.
The 313 people, who had been suspected of being members of Boko Haram, will be released after a ruling by a court in northeastern Borno state, the heartland of the insurgency, according to defence spokesperson Major General Edward Buba.
"The court ordered their release for want of evidence after the conclusion of investigations and other ancillary matters," Buba said during a media briefing in the capital Abuja. The cases were prosecuted by the Department of Prosecution, part of the Federal Ministry of Justice, and the people will be handed over to the Borno State Government for further action, he added.
Buba would not say where the suspects were being held or how long they had been in custody.
Nigeria has been running an amnesty program for jihadists who willingly surrender. The fighters go through a rehabilitation before being reintegrated into society, which is creating tensions in some communities.
Boko Haram grabbed headlines worldwide with its 2014 kidnapping of more than 270 schoolgirls from the town of Chibok, sparking a global campaign for their return dubbed #BringBackOurGirls. Next month is the tenth anniversary of the kidnapping and dozens of the girls have not been found.