The statement from an adviser to President Goodluck Jonathan comes after widespread allegations of Nigerian authorities carrying out indiscriminate arrests, unlawful detentions and extra-judicial executions in the fight against Islamist extremists over the last several years.
It was issued because the government said it wanted to further clarify a defence ministry statement this week promising to release certain suspects held in connection with "terrorism," including all women. The military had made no mention of children.
"Concerning the first batch, the emphasis is on women and children who have been in detention on suspicion of involvement and/or connection with insurgency in some parts of the country."
Islamist extremist group Boko Haram has previously demanded the release of women and children prisoners, though neither the defence nor government statement made any mention of the demand.
The promise to release some of those detained comes as the military carries out an offensive in Nigeria's northeast launched on May 15 seeking to end a violent insurgency underway since 2009.
"In recent weeks, residents of Borno state in northern Nigeria have told Amnesty International that mass arrests in the state capital Maiduguri have increased," it said, referring to the city where Boko Haram has been based.
"Individuals in military vehicles have been depositing bodies on an almost daily basis at mortuaries in the town. The government... Has not released any information pertaining to those deceased and deposited at the mortuaries.