Benin Republic fared worse as it has been kicked out of the competition because most of its players are over the age limit.
Nigeria will begin its campaign in the competition holding in Niger Republic today when it meets Burkina Faso by 4.00 p.m.
Among the remaining players in the Nigerian team are 15 outfield boys and three goalkeepers.
Coach Manu Garba had earlier denied that some of his boys were over the age limit, saying they passed the MRI scan in Abuja when it was reported that as many as 15 of the 40 players he had in camp failed the test.
As things stand, Nigeria will play with only the 18 players left in the squad.
Cote d’Ivoire is the other team in Group B following the disqualification of Benin, while Niger Republic, Ghana and Togo are in Group A.
After Burkina Faso, the Eaglets will tackle Cote d’Ivoire on Thursday in what appears the last game of the group.
A new format approved for the competition at the CAF Extra-Ordinary General Assembly, which took place in Rabat 13 months ago, means countries in each regional bloc gather in one country within the bloc to play a qualifying tournament, as against the old format of home-and-away qualifying series.
Only the winning team from each of the blocs (apart from the bloc of the defending champions that will produce two teams) will qualify for the final tournament, slated for Tanzania next year.