Following a general assembly last month, Chris Giwa claimed THAT he had been elected as the new president of the Nigeria Football Federation (NFF).
World governing body FIFA failed to recognise his appointment and set a deadline of 7.00am (GMT) on Monday September 8 for Giwa to step aside.
Nigeria were threatened with being kicked out of qualifying but on Monday Musa Amadu, general secretary of the FIFA-recognised NFF, claimed that the issue was now resolved.
"It has been a difficult time for our football but everything is over now," he told BBC Sport.
"Our attention should shift towards moving our football forward because the country's football has gone through a tough period."
Aside from matters off the field, Nigeria's campaign on the pitch started in far from ideal fashion, as Stephen Keshi's men went down 3-2 at home to Congo in their Group A opener on Saturday.
Next up for the defending champions is a trip to South Africa, who began in fine style with a 3-0 win over Sudan, but midfielder Sibusiso Vilakazi has warned against complacency.
"We just need to keep our feet grounded and the rest will follow," he said. "The players know what it means to represent one's country. They know that behind their backs that they are carrying the hopes of 52 million people."
Elsewhere in the group, Congo will look to build on their memorable opening-day win when they host Sudan.
Two African giants go head to head in Group D as Cameroon host Ivory Coast. Both sides began with victories against Congo DR and Sierra Leone respectively, and the latter pair meet in Lubumbashi aiming for their first points of the campaign.
Mali and Algeria were victorious in their Group B openers, and they will go head to head in Blida vying for top spot, while Ethiopia and Malawi meet in the group's other fixture.
Cape Verde Islands stole a march in Group F after beating Niger 3-1, and they will hope to make it two out of two at home to Zambia.
Mozambique host Niger in the other match in the pool, while in Group C Angola welcome Burkina Faso and Gabon visit Lesotho.
There is an all north-African clash in Group G as seven-time champions Egypt welcome Tunisia, while Senegal visit Botswana. In Group E, Ghana travel to Togo and Uganda take on Guinea.
