The delay means the men’s team are expected to arrive in Brazil less than 36 hours before their opening match.
“The money paid by the [sports] ministry for the charter flight did not hit airline’s account on Tuesday so they refused to fly the team to Brazil,” a source close to the Nigeria Football Federation (NFF) said.
They play Japan at 0100 GMT on Friday.
The problems seem to have happened due to the money having to go through different bank accounts and currency conversions.
“It is a cumbersome exercise but they should have started the process much earlier, which NFF was pointing out. This issue has nothing to do with the NFF,” the source explained to BBC Sport.
He added that everyone in the NFF was “disturbed” by the situation because Nigeria’s first game against Japan in Manaus is so soon.
The BBC has spoken to several players in the party, who say they do not yet know when they will be travelling.
One of the players explained: “We’ve been told to get ready to fly out in few hours but that’s been the story since last week.”
Nigeria, who are in Group B of the Rio Games alongside Sweden, Colombia and Japan, boast a proud Olympic record.
In 1996, they became the first African and non-European or South American team to win the gold medal.
They also finished runners-up at the 2008 Beijing Olympics, where current under-23 coach Siasia also coached the ‘Dream Team’ in China.