"President Goodluck Jonathan has directed that Nigeria withdraws from international competition for two years to enable the country to put its house in order," said special presidential adviser Ima Niboro.
However, Fifa rules clearly state that national associations can be expelled if governments are seen to be interfering with the way they operate.
"Fifa has sent a letter to the Nigeria Football Federation indicating that the government of Nigeria has until Monday at 6pm to cancel its direction to withdraw Nigeria's participation from all Fifa and Caf competitions for the next two years," said Fifa's communications director Nicolas Maingot on Friday.
"Also the management committee set up by the Nigeria government will not be recognised by Fifa.
If Nigeria are suspended, the country cannot participate in competitive matches or club games in African competitions, as well as a host of financial ramifications.
"A suspension goes beyond the suspension of the national teams," added Maingot. "It also freezes financial help and no referees can participate in international competition."
Fifa executive committee member and former Nigeria government minister Dr Amos Adamu will be in the country on Monday "for last mediation attempt".
The governing body's president Sepp Blatter had already warned French president Nicolas Sarkozy of possible sanctions after Sarkozy pledged to personally lead an investigation into France's acrimonious World Cup campaign.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.