Nigeria could be suspended by FIFA after the country's football federation leaders were removed from office and its president was arrested on returning from the World Cup.
FIFA warned Nigeria's government on Friday it must reinstate the federation's executive committee by Tuesday or risk a ban.
"FIFA has also taken note of the detention of NFF President Aminu Maigari carried out by representatives of the Department of the State Security Service," the governing body said in a statement.
The turmoil follows Nigeria's 2-0 loss against France in the second round on Monday.
Nigeria's government also reacted aggressively after the Super Eagles' 2010 World Cup exit. Then, state President Goodluck Jonathan threatened to shut down the national team for two years before FIFA intervened.
FIFA rules protect its 209 member federations from government interference, and a suspension bars teams and officials from taking part in international matches and meetings.
A High Court session in the Nigerian capital Abuja on Thursday served a restraining order on the country's football leaders.
The sports ministry also appointed one of its own officials to run the football body
FIFA wrote to the NFF "expressing its great concern over different actions taken by Nigerian public authorities," it said.
An election meeting reportedly scheduled in Abuja on Saturday would not be recognized, FIFA said.
FIFA said an official football congress was called for Aug. 26 and "only decisions and persons elected then will be considered legitimate."
Nigeria reached the World Cup knockout rounds for the first time since 1998 after beating Bosnia-Herzegovina 1-0 and drawing 0-0 with Iran. It also impressed when losing 3-2 against Argentina.
Its next competitive matches are 2015 African Cup of Nations qualifiers in September.