BBC Sport has learned the problem lies in the interpretation of the bonus structure, with the players believing they will only receive $10,000 for their win 1-0 over Bosnia-Hercegovina and $5,000 for the 0-0 draw with Iran.
The players’ understanding was they would receive a $30,000 payment for qualifying from the group.
However, it is believed the Nigerian Football Federation’s offer to the players includes the agreed win and draw bonuses plus 30% of the prize money due from Fifa for reaching the knockout stage.
This is understood to rise to 40% of the prize money from Fifa if Nigeria were to win their round of 16 match, 50% for a quarter-final victory, 60% for a win in the semi-final stage and 70% for lifting the trophy.
While all parties work to find a resolution to the misunderstanding, coach Stephen Keshi has insisted it will not affect the team’s performance.
And it has been confirmed to the BBC that the players will travel to Brasilia on Friday as scheduled and will train in the evening and over the weekend.