Senior Special Adviser on Media and Publicity to President Muhammadu Buhari, Mallam Garba Shehu, confirmed the release and said the girls are in the custody of the Department of State Services, DSS.
Shehu confirmed the release of the girls in his twitter handle on Thursday.
Reports filtered in early Thursday morning that the girls have been released by the Boko Haram militants who dropped the schoolgirls off earlier on.
The release of the 21 girls comes as President Muhammadu Buhari began a three-day trip to Germany.
President Buhari is going to Germany to discuss assistance for the rebuilding of the northeastern part of Nigeria ravaged by Boko Haram.
More than 270 girls were abducted on 14 April, 2014 at the Government Girls Secondary School, Chibok in Borno State.
The girls were reported to be writing their final exit examination when the insurgents burst into their hostel in the middle of the night and abducted them.
Some of them had escaped, leaving no fewer than 219. The abduction sparked world outrage.
The federal government had adopted both diplomacy and military force, but had yet to rescue the schoolgirls.
Alhaji Lai Mohammed, Information and culture minister recently explained that the government had made three diplomatic moves to secure at least 50 of the schoolgirls.
He reported that the government went to the extent of trying to exchange some Boko Haram sect prisoners for the girls as requested by the leadership of the insurgents.
All the three attempts failed because the insurgents failed to honour the meetings for the exchange.
Chibok-based Socio-cultural group on the platform of Kibaku Area Development Association, had commended the willingness of the federal government to negotiate and secure release of abducted schoolgirls from Boko Haram.
In a recent interview with the News Agency of Nigeria (NAN) in Maiduguri, the National Secretary of Kubaku, Mr Muhammad Askira, made the commendation.
Askira said that the hope of the parents to reuniting with their wards was redeemed following the pronouncement of the federal government willingness to negotiate with Boko Haram.
His words; “It is the obligation of the federal government to use every available opportunity given to secure the rescue of our daughter.
“If the Boko Haram are sincere with what they have said, we believed our girls would be surely rescued.
“We are forever indebted and grateful to President Muhammadu Buhari for his empathy, commitment and political will in the fight against the insurgency.
“Kubaku” is the umbrella body of the Chibok communities which include Ymir Ali, Njoma, Gwandan Rimirgu, Mikabu as well as Chanchan Bulguma in Askira Uba axis of southern Borno State.