"FIFA has learnt that the Iraqi Olympic Committee announced the dissolution of the governing board of the Iraqi Football Association (IFA)," a FIFA statement said.
"The basis on which such a decision could be taken is incomprehensible to FIFA. This stands in total contradiction with IFA and FIFA statutes."
The leaders of Iraq's Olympic committee and the Iraqi Football Association have been embroiled in a power struggle for control of the sport for at least a year.
Olympic committee members blame the IFA for a continuing FIFA ban on Iraq hosting international matches due to lingering insecurity.
FIFA this year allowed Iraq to host its first friendlies since the 2003 US-led invasion, and Iraq beat Palestine in two matches played in the northern city of Arbil and in Baghdad. But the general ban remains in place.
The Olympic committee has demanded the IFA elect a new governing board but the football federation has refused to do so. Olympic committee members were enraged when FIFA intervened to extend the mandate of the IFA's board.
"We will not reverse our decision to disband the Iraqi Soccer Federation," Samir al-Moussawi, an official of the Olympic committee, told Reuters, adding the panel would endeavour to explain its position to FIFA.
Iraq has been given 72 hours to restore the IFA or the matter will be referred to the FIFA Emergency Committee which would almost certainly result in suspension.
"FIFA appeals once more to all stakeholders in Iraq to respect the autonomy of sport in general and the IFA in particular and to allow IFA to conduct its affairs according its statutes and those of FIFA," the statement added.
The deputy head of the IFA, Najih Hmoud, said the Olympic committee's actions were "illegitimate and illegal".
"This decision is wrong and damages the public interest of Iraq," he said.
