FIFA will suspend Nigeria from world football unless the country's government overturns its ban on the national team by Monday.
"Failure to do so will result in the suspension of the NFF," Maingot said.
FIFA rules protect football from government intervention.
Jonathan said on Wednesday that he was banning the team and dissolving the NFF management board after the country's first-round exit from the World Cup.
Jonathan also ordered a probe into alleged financial corruption at the federation.
Nigeria was knocked out of the World Cup in South Africa last week after losing two of its first-round matches and scraping a 2-2 draw with South Korea.
The Super Eagles, one of a record six African teams at the tournament, finished last in Group B, while Argentina and South Korea advanced.
