The Super Eagles deliberately missed a training session in Brazil in 2014 in protest at the non-payment of a bonus for qualifying.
Coach Gernot Rohr has said a similar situation would “be bad for our preparation”, with the team already through to the tournament in Russia next year.
Now, the NFF said it would “ensure that negotiations with the players… are firmly concluded and agreement signed before the end of the year”.
That would help “stable preparations and credible participation at the World Cup finals without any distractions”, it added after an executive committee meeting that ended late Thursday.
There was no immediate indication of how much money the players would be paid.
But in 2014, the country’s then sports minister was forced to charter a jet and fly to South America with nearly $4m in cash.
Observers expect at least the same amount this time round.
All 37 players used in qualifying are entitled to a share of a $12.5m bonus from world governing body FIFA for making the finals.
Nigeria’s best performance at the World Cup was in 1994 and 2014, when they reached the last 16.
The NFF said a “comprehensive plan of action” for the side’s preparations would be announced after the World Cup draw in Moscow on December 1.