His initial contract paid him $70,000 a month, but it is understood the new agreement will have his monthly pay at $50,000 after the federation said they could no longer afford his previous salary.
He has been handed the target of leading the Super Eagles to at least the semi-finals of the Africa Cup to be hosted by the Ivory Coast in January.
The three-time African champions have 12 points from five qualifying matches and have already secured a place at the tournament.
However, they will need at least a point against Sao Tome and Principe next weekend to win their group ahead of second-placed Guinea Bissau, who are on 10 points and play at home to Sierra Leone.
Nigeria has called up several uncapped players including Victor Boniface, Gift Orban and Jordan Torunarigha for the match.
Boniface has so far netted four goals at new Bundesliga club Bayer Leverkusen, while Orban has hit 26 goals for Belgian club Gent in all competitions since January.
There is also a recall for Portugal-based left back, Bruno Onyemaechi, Tyronne Ebuehi, defensive midfielder Raphael Onyedika and defender Jamilu Collins, who has returned from a long-term injury.
AFP
