Chris Giwa looks to have given up his claim to be Nigeria Football Federation president in a move that coincides with a deadline set by FIFA.
The ultimatum was set last week for him to step aside or face a FIFA ban.
A suspension could have led to Nigeria missing Wednesday’s Africa Cup of Nations qualifier in South Africa.
The Confederation of African Football (CAF) said last week that the Super Eagles would be kicked out of the 2015 qualifying campaign should they fail to play the fixture.
“It has been a difficult time for our football but everything is over now,” General Secretary of the FIFA-recognised NFF, Musa Amadu told BBC Sport.
Amadu resumed work at the federation’s offices in Abuja on Monday.
“Our attention should shift towards moving our football forward because the country’s football has gone through a tough period,” he added.
“The next step is to have an extra-ordinary assembly that will set a date for elections for the new executive committee.
“It is important to emphasise that this will not happen beyond September 25, as directed by FIFA.”
World football’s governing body had reiterated last week that it did not recognise Giwa’s election on August 26 and set a deadline of Monday 0700 GMT for him to step aside.
The latest development means the NFF board, as it was on August 25, with Aminu Maigari as president, can now begin to plan for elections to be held as soon as possible.
Nigeria was banned from global football for nine days in July for government interference in the running of the football federation when Maigari was forced out of his post by a court ruling.
After his reinstatement, he was voted out of office by the NFF’s executive committee a few days later. However, FIFA did not accept this and Maigari was once again back as president in August.