The federation had invited Shola Ameobi of Newcastle and Millwall FC's Danny Shitu for the AFCON competition holding in South Africa between January 19 and February 10.
The Chairman, Technical Committee of NFF, Mr Chris Green, who confirmed this in Port Harcourt said if by January 5 Ameobi and Shittu failed to report to the Eagles' camp, the federation would write to FIFA against the clubs.
"Now, for Danny Shittu and Shola Ameobi, as far as we are concerned, we do not want that matter to distract us because the coach is ready to work without the players.
"But again, the football federation shall consider such attitude as quite unwholesome on the part of the players as well as their clubs because as it appears, it's the clubs that are pushing for these players not to honour the invitation to play for their country.
"So, of course, we are going to take the matter to FIFA; we are going to write appropriately; we are not going to lie low because, at least, let's do what is right, that we should not be taken for granted.
"After all, these players were found in Nigeria, these players are from Nigeria and they also desire to play for Nigeria.
"So, what is the problem? Why would they have to stop them, using underarm tricks to stop them. That will not be right," he said.
Green said both Newcastle and Millwall had not communicated with the federation officially over the inability of these players to play for Nigeria.
However, the NFF official said the coaching crew of the Super Eagles had other players to replace Ameobi and Shittu if they failed to report to camp.
He said more players would join others already in camp in Faro, Portugal, and that the team would play a friendly match with Cape Verde before the tournament, in South Africa.