It follows last week's regional high court ruling that Chris Giwa should be installed as the NFF's President and that the Fifa-recognised head, Amaju Pinnick, be sacked.
Fifa warned that the country could face sanctions - including a ban - if a decision of the Federal High Court in Jos from Friday is implemented.
In a letter dated 11 April 2016, Fifa's acting secretary general Markus Kattner said the ruling by a Jos federal high court is classed as "interference."
"The decision of the Federal High Court in Jos, if implemented, would likely be considered as interference in the internal affairs of the NFF and the case would be brought to the highest authorities of Fifa for consideration of sanctions, including the suspension of the NFF," the letter read in part.
"All members associations have to manage their affairs independently and with no influence from third parties. In addition and according to article 68 of the Fifa Statutes, recourse to ordinary courts of law is prohibited unless specifically provided for in the Fifa regulations.
"Furthermore, it is the duty of each member association to ensure that these provisions are implemented by its members and possibly take sanctions against those which fail to respect these obligations.
Fifa also acknowledged that it is the second time that Chris Giwa has resorted to legal action as well as a futile appeal at the Court of Arbitration for Sport (Cas) in his attempt to run the country's football affairs.
"We would like to stress that the plaintiff in question already filed an appeal in relation to the same matter with the highest judicial Sport authorities, the Court of Arbitration for Sport (CAS), and that said appeal was dismissed by the CAS on 18 May 2015."
The NFF has appealed against the court ruling, insisting that Pinnick is still the head of the federation while Giwa's faction and all other non-NFF staff were denied access into the football house by police in the capital Abuja on Monday.
Fifa, however, has taken a dim view of the development and warned that Nigeria risked suspension if the sacked officials are not reinstated as soon as possible.
The ongoing power struggle means Nigeria's Olympic team is at risk of being banned from Rio this year, and the Super Eagles could be denied a chance to qualify for the 2018 World Cup in Russia.
The qualifying draw takes place in June.