Football's world governing body had earlier issued an ultimatum warning that the Nigerian Football Federation would be barred from all FIFA-related activities if the government did not agree to change its decision by Monday evening.
"Mr President will not rescind the decision because it's the best decision for football development in Nigeria," a presidency source said.
"Mr President and his team had weighed the consequences of this decision and arrived at this decision as in the interest of the nation. We need to restructure and reorganise our football for effective and commendable results."
The ultimatum from FIFA, which does not tolerate government interference in football matters, came after Nigeria's President Goodluck Jonathan withdrew the Super Eagles from international competition for two years on Wednesday.
It followed the teams' poor World Cup performance which saw them knocked out in the first round after failing to win a game.
"FIFA will today send a letter to the Nigerian football federation indicating that the government of Nigeria has until Monday to cancel its decision to withdraw Nigeria's participation in all FIFA and CAF organised football competitions," FIFA spokesman Nicolas Maingot told a news briefing on Friday.
After meeting the country's World Cup organising committee, Jonathan also said the accounts of the committee should be audited, and named an 11-member caretaker committee to sort out the administration and management of the game.
If the Nigerian government fails to heed to FIFA's ultimatum, it risks getting cut-off from all FIFA activities, including junior and female competitions, and also FIFA funding to the football association.
"A suspension goes beyond the suspension of the national team, it also involves the freezing of the financial help and no referees can participate in international competition," Maingot said.
They also qualified for the upcoming women's world championships at under-20 and under-17 level and their top club side Heartland is to play in the African Champions League group phase later this month.
"FIFA's $1 million was used for things that did not benefit the team in terms of preparation," he said, adding the taskforce had handed the matter over to Nigeria's sports commission and he could not
