According to the world football body, failure for Nigeria to abide by the directive would see the country banned from all footballing activities.
Fifa is cautioning the football ruling bodies in Ghana and Nigeria to solves various issues confronting their football or risk being hit with suspensions.
Nigeria is still experiencing a power struggle as Chris Giwa and Amaju Pinnick factions are yet to settle their differences. A situation which led to the delay in resumption of the Nigeria Professional Football League.
Fifa sees Pinnick as the legitimate head of the NFF following his win in the election held on 30 September 2014.
According to the world football body, failure for Nigeria to abide by the directive would see the country banned from all footballing activities.
However, Nigeria U20 women who have progressed to the last eight of the U20 Women's World Cup will be allowed to carry on provided they make the semi-final.
"Two decisions of the Bureau of the Fifa Council in relation to undue influence in the affairs of the Nigeria Football Federation and the Ghana Football Association have been notified on 13 August 2018," read a statement from Fifa.
"In line with art. 16 par. 1 of the Fifa Statutes, the Bureau of the Fifa Council decided that if by Monday, 20 August 2018, at 12:00 (CET), the Nigeria Football Federation (NFF) offices are not handed back to the legitimate NFF executive committee under President Amaju Melvin Pinnick, who was duly elected on 30 September 2014, the NFF will be suspended with immediate effect for contravening art. 14 par. 1 i) and art. 19, as well as art. 14 par. 1 a) of the Fifa Statutes. The suspension would be lifted only once the NFF, under President Amaju Melvin Pinnick and General Secretary Mohammed Sanusi, confirms that it has been given back effective control of the NFF and its offices.
"Furthermore, the Bureau decided that if the suspension of the NFF takes effect, the Nigerian team currently competing in the Fifa U-20 Women’s World Cup France 2018 will still be allowed to continue to participate in the tournament on an exceptional basis given that the tournament is underway."
Ghana, on their own part, are battling to get their football back on its feet after an exposé released in June by undercover journalist Anas Aremeyaw Anas, culminating in the resignation of former Ghana Football Association boss Kwesi Nyantakyi.
The government have halted all football-related activities in the country and have a court case meant to cleanse the battered GFA - a decision that does not go well with Fifa who had installed a two-man liaison to run the nation's football.