Army chief Lt. Gen. Kenneth Minima says they "have been investigated and found to be free of all suspected incrimination."
He handed them over Monday in northeastern Maiduguri city to Borno State Gov. Kashim Shettima to be reunited with their families.
Some freed women said they are widows. Others said they were arrested because their brothers were suspected Boko Haram members.
President Muhammadu Buhari's government says it's investigating an Amnesty International report that last month charged Nigeria's military for the deaths of 8,000 detainees, some killed outright and others who died of starvation and suffocation.