Nigeria has narrowly escaped an international football ban after its government responded to a FIFA ultimatum shortly before a suspension took effect on Monday.
Football's world governing body had said that it could suspend the country on Monday should Amaju Pinnick be displaced.
Pinnick, who was elected head of Nigeria Football Federation in 2014, was in a stand-off with Chris Giwa, who had appealed the result and won a favourable court ruling in June.
"The suspension of the NFF will not take effect," Fifa said in a statement.
"Fifa received confirmations that the legitimate leadership of the NFF under President Amaju Melvin Pinnick and General Secretary Mohammed Sanusi has been given back effective control of the NFF and its offices."
Earlier on Monday, Laolu Akande - the Special Assistant to the Nigerian Vice President - tweeted: "The Federal Government has already conveyed to Fifa its firm position recognising the Pinnick-led NFF as the current and only NFF executive."
Last week, Fifa - which does not accept governmental interference in the running of football - had threatened to suspend Nigeria over the long-running leadership dispute.
Giwa has continued his fight for control of the NFF despite currently serving a five-year ban from all football related activity that has been ratified by Fifa.
The NFF are due to hold elections on 20 September.