Fifa has issued a warning to Nigeria: comply with the rules or face suspension.
Football's world governing body has given Nigeria's government until 8 July to reinstate the sacked Nigeria Football Federation (NFF) executive committee.
The NFF was dissolved on Thursday and replaced by a sole administrator - a move the government said was essential while legal proceedings against the country's football authority were ongoing.
The situation was compounded 24 hours later when the NFF president Aminu Maigari was arrested upon his return from the World Cup.
All this comes in the wake of a high court ruling which granted 'an interlocutory injunction' to suspend Maigari, his executive committee and the NFF congress.
Fifa, however, has taken a dim view of the development and warned that Nigeria risked suspension if the sacked officials are not reinstated.
Under Fifa statutes, national football associations must not be subject to government control.
"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 Zurich-based governing body said in a statement.
The statement went on: "FIFA will not recognise any person or organ not elected in compliance with the NFF statutes (article 17, par 2 and 3 of the FIFA 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 26 August 2014 and only decisions and persons elected then will be considered legitimate.
"FIFA is also aware that the Minister of Sport has appointed an assistant director to take charge of the NFF. It is alleged that the members of the NFF have been convened to attend an Extraordinary Congress on 5 July 2014 in Abuja.
"FIFA has reminded the NFF that all FIFA member associations have to manage their affairs independently and without influence of any third parties as clearly stipulated in articles 13, par. 1 and 17, par. 1 of the FIFA Statutes. The above mentioned actions are preventing the NFF from managing its affairs independently and are considered by FIFA as undue interference in the NFF affairs.
"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 8 July 2014 the case will be referred to the appropriate FIFA bodies for sanctions, including the potential suspension of the NFF."
Fifa rules protect its members from government interference, and a suspension bars teams and officials from taking part in international matches and meetings.