President Goodluck Jonathan announced on Wednesday he was suspending the team from playing in international competition for two years following their poor performance at the tournament in South Africa, where they finished last in their group with a solitary point.
Within hours of the announcement from Abuja, FIFA warned of possible sanctions.
"FIFA has a very clear position on government interference or, better said, the independence of sporting bodies," FIFA spokesman Nicolas Maingot said on Thursday.
If Nigeria's government presses forward with its edict, FIFA are almost sure to ban the country from all football activity, a sanction which would hit not only their men's side but also youth teams and clubs participating in international competitions.
Nigeria have qualified for the upcoming women's world championships at under-20 and under-17 level and their top club side Heartland play in the African Champions League group phase later this month.
A FIFA ban would also cut access to its development courses and stop the annual payment of $250,000 each of its member associations receives, cash that is much needed by Nigerian football.
ALLEGED CORRUPTION
Football analysts said the presidential decision had been a knee-jerk reaction to the disappointment of the World Cup failure and the consequences had not been properly considered.
"This, to me, is another fire-brigade move that will bring more harm than any good to our football," wrote columnist Michael Effiong in the Times of Nigeria on Thursday.
"You do not need to withdraw from FIFA competitions to build a formidable national team, it takes careful planning, hard work and vision."
The influential KickOffNigeria.com website said the government wanted to clean up alleged corruption in the game in Nigeria.
"In the event, the Nigerian government's demands are clear: that FIFA must accept the removal of the current Nigerian Football Federation (NFF) leadership, with transparent elections to be held to bring in a new team," said commentator Colin Udoh.
Nigeria's president also ordered an audit of the NFF accounts.
"If any financial misappropriation is discovered, all officials responsible will be held accountable," his spokesman Imo Niboro said.
"The problem of Nigerian football is structural. We need to reorganise the structures and there is need to withdraw from all international football competition so that we can put our house in order," he added.
The federation had earlier apologised to the "federal government and all football-loving Nigerians for the early ouster of the Super Eagles from the World Cup" but said the current leadership had achieved more success in FIFA competition than any previous regimes.
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