The Super Eagles are fully expected to travel to Brazil later than scheduled to compete in the tournament, but internal wranglings have sent their plans into chaos
The players were each offered half of the normal $5,000 (€3,800) bonus after the 1-1 draw on Wednesday which has led to murmurings of a revolt within the camp.
Players are also unhappy with the treatment of former player and assistant coach Silvanus Okpala and other members of the backroom team.
The cash-stricken NFF continue to cut back on costs following an expensive Africa Cup of Nations campaign which has meant staff have been reduced from 17 to nine.
The team were due to travel to South Africa for a connecting flight to Brazil this afternoon, but while they have not boarded the plane, they are fully expected to travel to the event on Sunday and complete their tournament obligations.
Nigeria are set to play Tahiti in their opening game of the tournament on Monday.