"During the period of suspension, the NFF will not be able to be represented in any regional, continental or international competitions, including at club level, and also not in friendly matches," the Fifa statement added.
Nigeria's ban from international football leaves their weekend's Africa Cup of Nations qualifier against Guinea in Conakry in doubt.
The world governing body said the ban follows a bid by Nigeria's Minister of Sports to restart the league without relegations from the previous season.
The decision by the Nigeria Sports Commission to force the NFF's secretary-general Musa Amadu to stand down from his position did not go down well with Fifa.
A court action barring the newly-elected members of the NFF also drew the ire of the world governing body.
The NFF board led by Aminu Maigari has not been able to operate because a Lagos High Court ruled that the elections that brought him to power in August were null and void.
A group known as the National Association of Nigerian Footballers (NANF) dragged the newly-elected board of the NFF to court for allegedly defying a court not to proceed with the polls of 26 August.
Subsequently, Nigerian Fifa committee member executive Amos Adamu, NFF president Maigari, his vice-president, Mike Umeh as well as acting secretary-general of the NFF, Musa Amadu were hauled before the court.
The NFF has been dogged by controversies since the team's elimination in the first round of the World Cup in South Africa in June.