Several developments led to FIFA imposing the suspension yesterday, including court actions against elected members of the NFF executive committee, the federation's general secretary stepping down on orders from the government-run National Sports Commission, and the decision of the sports minister to start the Nigerian football league without relegation from the previous season.
FIFA rules prohibit government interference with national football governing bodies.
Nigeria had been due to play in Guinea in its second qualifier in Group B the African Cup on Sunday.
FIFA says the suspension will last until "the duly elected NFF executive committee is able to work without any interference," meaning none of the country's teams are allowed to take part in any competition "regional, continental or international."
Calls to NFF officials seeking comment were not answered.Nigeria's federation was threatened with a similar ban in July when the country's president, Goodluck Jonathan, said he would pull the national team out of competition because of its poor showing at the World Cup in South Africa. Jonathan eventually backed down following an ultimatum from FIFA.
However, FIFA said at the time it would continue monitoring Nigerian football for possible interference from the government.