The NFF is unhappy at the possibility Nigeria will be deprived of the defender's services when the tournament begins on January 19.
Shittu was named in coach Stephen Keshi's provisional 32-man squad but Lions manager Kenny Jackett has hinted that his player will reject the opportunity to feature in the competition.
Newcastle striker Shola Ameobi was also included in the squad, but Magpies boss Alan Pardew says his player will not be taking part either.
"These clubs are not only disrespecting Nigeria but FIFA and [African governing body] CAF as well," NFF board member Chris Green told BBC Sport.
"The rules are clear on international games approved by FIFA so we consider these comments as not only ridiculous but totally disrespectful."
Both clubs could face sanctions if they do not allow their players to be considered for selection, but the Championship outfit said they would discuss the issue with their player first.
Governing body rules would prevent Shittu from representing Millwall for the duration of the African Cup of Nations.
The relevant ruling also states: "This restriction on playing for the club shall, moreover, be prolonged by five days in the event that the player, for whatsoever reason, did not wish to or was unable to comply with the call-up."
Green added: "We will further push for additional sanctions - we understand these clubs employ our players but they are also international footballers. Rules are rules. Newcastle and Millwall must understand the basics [of] why they exist."
Millwall have also appealed against the red card dished out to Adam Smith in last Saturday's 2-1 home defeat to Barnsley.
The on-loan Tottenham defender was dismissed in the 54th minute following a challenge on David Perkins.
The Lions expect to hear the outcome of the appeal on Thursday afternoon, following a meeting of the FA's Disciplinary Committee.