Nigeria have missed their flight to Brazil because of a row over players' bonuses, The Super Eagles are due to play their first match in the tournament on Monday but they remain in Namibia after Wednesday's World Cup qualifier.
Nigeria's players are unhappy after they were offered a $2,500-a-man bonus for the 1-1 draw in Windhoek, insisting they want double that amount.
And it appears they have refused to travel while the dispute continues.
It raises questions over whether the African champions will participate in the tournament which runs from 15-30 June.
Nigeria Football Federation (NFF) president Aminu Maigari met the team on Wednesday night in Windhoek to explain to them that the organisation has no choice but to make drastic cuts in its expenditure.
Last week, local media reported there was a players' revolt in Kenya over the bonus when the Super Eagles beat the home team 1-0 in another 2014 World Cup qualifier.
The players wanted to be paid $10,000 each for the win in Nairobi but several officials rejected the claims.
The cash-strapped NFF has been forced to cut back on backroom staff of the various national teams, including the Super Eagles, after an expensive Africa Cup of Nations campaign in South Africa.
They had even considered pulling out of the 2014 Championship of African Nations (CHAN) for players in the local league because of poor finances before a change of heart.
Nigeria were due to fly out of Windhoek to Johannesburg on Thursday bound for Sao Paulo before continuing their journey to Belo Horizonte, venue of their opening match of the Confederations Cup against Tahiti