In November, the Super Eagles needed a win at home against group winners South Africa to qualify for the 2015 tournament, but instead they could only draw 2-2 in the southern coastal town of Uyo, allowing Congo to snatch second place.
Coach Stephen Keshi, who was blamed for the team's latest woes and asked to quit, will now be given a new contract after his initial agreement ended with the Eagles' exit from the 2014 World Cup in Brazil.
NFF president Amaju Pinnick said Keshi will be given a lot more support to improve the three-time African champions' performances.
“Keshi has won everything; he just needs to be strengthened in terms of building his capacity and that is exactly what we intend to do,” said Pinnick.
“It's like when you are building a house and you feel that the house needs to be enhanced, so you put other structures for enhancement and that's what we are going to do.”
He added: “Keshi is going to be offered a new contract. But in the contract we are going to have certain clauses for him to work with the technical study group, work with the technical committee and work with the technical department.
“And making sure in terms of player selection, there is science of players which means fitness and so many other things.”
Warri Wolves defender Azubuike Egwuekwe said he is encouraged that the NFF have moved ahead with plans to re-organise the team.
“We know we are better than most of the teams who will be at this Nations Cup, but we made mistakes along the line and we must thank Nigerians for forgiving us and also thank the NFF for being forward-looking despite our elimination,” he said.
“We will reward the country next time with another Nations Cup win.”
Nigeria assistant coach Daniel Amokachi said such failure to qualify for the CAN must never be repeated.
“We won't be there to defend our crown, that's football for you. We now have to work harder and look to qualify for the next edition of the tournament,” said Amokachi, who has won the competition both as a player and a coach.
The NFF have moved quickly to assemble a team of players from the domestic league for a series of top international friendlies including one against Nations Cup-bound Ivory Coast, which they lost 1-0.
The country's Under-17, Under-20 and Olympic teams are now in training camp for major tournaments later this year as officials plan to draft outstanding players from these teams in place of the likes of Joseph Yobo and Peter Odemwingie.
