According to a statement from FIFA released on Friday, the country's State Security Service arrested Nigeria Football Federation (NFF) president Aminu Maigari, while the Nigerian government have installed Lawrence Longyir Katiken to run the national governing body.
FIFA warned the NFF that they could be banned from international football if they cannot prove their independence from the Nigerian government.
"FIFA has reminded the NFF that all FIFA member associations have to manage their affairs independently and without influence of any third parties," the statement on FIFA's website read.
The statement continued: "FIFA will not recognize any person or organ not elected in compliance with the NFF statutes...and therefore it will not consider the appointment made by the Minister of Sports.
"An elective Congress has been duly convened by the NFF for August 26, 2014 and only decisions and persons elected then will be considered legitimate.
"The NFF has been asked to relay FIFA's position to the relevant authorities and inform them that if the aforementioned NFF officials are not fully reinstated by Tuesday July 8, 2014 the case will be referred to the appropriate FIFA bodies for sanctions, including the potential suspension of the NFF."
Nigeria reached the round of 16 at the FIFA World Cup in Brazil before being eliminated by France.
