The Super Eagles were due to train in Campinas at 6pm on Thursday, but with their bus ready to leave, the squad failed to turn up.
Media Officer Ben Alaiya explained that the players were 'in a meeting' and would come out for training after.
An hour later, the bus was re-parked with officials saying training had been cancelled.
KickOffNigeria.com understands that the players wanted to be paid the appearance fee agreed with the federation for making it past the World Cup group stages.
Prior to the meeting however, the NFF Geneural Secretary Musa Amadu, had left São Paulo for Nigeria.
A federation official told KickOffNigeria.com that he had left to get more money to prosecute the next round.
"Funds were only released for the group stages, so he has gone to get more for the second round," the official said.
However, Amadu is not expected to return before the round of 16 fixture against France.
The squad are due to leave for Brasilia on Friday afternoon ahead of their last 16 meeting against France. It is not yet certain if they will travel.