Nigerian sports minister Tammy Danagogo on Thursday appointed Lawrence Katiken as sole adminstrator of the NFF.
The move comes in the wake of Nigeria’s World Cup campain which came to an end on Monday with defeat to France in the last 16.
Danagogo acted after a high court in Plateau State granted an injunction stopping elected NFF president Aminu Maigari, his executive committee and the NFF congress from office.
This represents direct interference by government in football, which has in the past incurred worldwide bans handed down by FIFA.
Nigeria were threatened with a FIFA ban in 2010 just after the Super Eagles crashed out of the 2010 World Cup hosted by South Africa.
This was as a result of the federal government’s decision to withdraw the country from all international competitions for two years and sack the NFF management.
The government also called for a corruption probe of the NFF.
However, Nigerian President Goodluck Jonathan will later rescind this decision for FIFA to spare the country.
But later in 2010, the FIFA hammer finally fell on the country when top Nigeria FA officials were dragged before a court.
The ban was only quashed when the court ruling was set aside.
Nigeria reached the knockout stage of the World Cup in Brazil for only the third time in their history after 1994 and 1998.
Last year, the country also won the Africa Cup of Nations as well as a fourth FIFA U17 World Cup.