Fifa, however, has criticised the move, claiming it goes against the organisation's principle of country's football associations being independent bodies and expressing concern over the outside interference.
"Fifa has sent a letter to the Nigeria Football Federation (NFF) expressing its great concern over different actions taken by Nigerian public authorities that affect the NFF," its statement read.
"Fifa has learnt from various sources that the NFF has been served with court processes and that consequently an order restraining the President of the NFF, his executive committee members and the NFF congress from running the affairs of Nigerian football has been granted by a High Court of the Federal Republic of Nigeria.
"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. Furthermore, Fifa is also aware that the Minister of Sport has appointed an assistant director to take charge of the NFF.