The ban means no Nigerian team, including club sides, can play internationally, after FIFA acted on a warning they would take action if the NFF's sacked executive committee was not reinstated.
The move comes in response to a court order which led to the Nigerian Minister of Sports appointing a senior member of the civil service to take over the running of the NFF after Nigeria were knocked out of the World Cup finals in Brazil.
Any government interference in national football associations is forbidden by FIFA and they have taken a tough stance.
A statement from FIFA's emergency committee read: "The FIFA Emergency Committee has decided to suspend the Nigeria Football Federation (NFF) with immediate effect, on account of government interference.
"The decision follows a letter sent by FIFA to the NFF on 4 July 2014, in which it expressed its great concern after the NFF was served with court proceedings.
“Consequently an order preventing the president of the NFF, the NFF Executive Committee members and the NFF Congress from running the affairs of Nigerian football was granted by a High Court of the Federal Republic of Nigeria.
"The said court order compelled the Nigerian Minister of Sports to appoint a senior member of the civil service to manage the NFF until the matter was heard in court, without giving any date for such a hearing.
"The authorities then appointed a person who decided to convene an extraordinary general assembly on 5 July 2014. This extraordinary general assembly was convened in violation of the NFF statutes.
"Originally, an elective congress had been planned by the NFF to take place on 26 August 2014.
"The suspension will be lifted once the court actions have been withdrawn and the properly elected NFF Executive Committee, the NFF general assembly and the NFF administration are able to work without any interference in their affairs."
FIFA acted after its warnings went unheeded with an extraordinary general assembly of the federation taking place in Abuja at the weekend without NFF chief Aminu Maigari, his executive committee or the NFF congress having been restored to power.
Maigari was arrested on his return from Brazil, where Nigeria reached the second round before losing 2-0 to France in the last 16, before he was later released.
The FIFA ruling means the Nigeria team will be prevented from competing in the FIFA U20 Women's World Cup in Canada next month, unless the suspension is lifted by July 15.