The football governing body has given the African nation until Tuesday to reinstate the NFF board, after it was dismissed for alleged financial offenses.
The NFF, led by Aminu Maigari, was sacked by a Nigerian court on Saturday after it was found guilty of misappropriating funds, manipulating its own regulations and handling the Super Eagles' bonus controversey in Brazil in an unacceptable way. Maigari has since been detained by the Nigerian authorities.
After the hearing, a statement - signed by NFF vice president Obinna Ogba - was released which confirmed the drastic actions and alleged that the previous administration had brought embarrassment to the nation.
"The extraordinary congress unanimously endorsed the dissolution of the Aminu Maigari-led NFF executive committee, and immediate termination of the employment of all management staff," the statement read. "The congress also endorsed the dissolution of the boards of the Nigeria National League, Nigeria Women League ans the Nigeria Nationwide League.
"Congress bemoaned the unfortunate incident of the international embarrassment suffered by the Nigeria nation at the 2014 FIFA World Cup, by failure of the Aminu Maigari-led NFF to fully and firmly resolve issues of finance with the Super Eagles ahead of the championship.
"Congress accused the Maigari administration of abuse of NFF statues in its constitution of the NFF electoral committee, by altering the list of persons approved by the congress at the 2013 general assembly."
FIFA, however, has criticized the move, claiming it goes against the organization'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.
"FIFA has reminded the NFF that all Fifa member associations have to manage their affairs independently and without influence of any third parties.
"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 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 26 August 2014 and only decisions and persons elected then will be considered legitimate," Fifa concluded.
However, Nigeria's sports minister Tammy Danagogo has defended the government's actions.
"We will do our best to make Fifa know that there has been no government interference. We have no such intention," he said. "And I can assure you that we will not interfere beyond doing what is legally required by Fifa rules, and that we will ensure that there is a peaceful atmosphere.