They had already been held up in Atlanta, USA, because of a problem with the payment for their flight.
"The players were uncomfortable with the size of the plane," team media officer Timi Ebikagboro told BBC Sport.
He said they would leave on a bigger plane and arrive in time for kick-off against Japan (01:00 GMT Friday).
"The [Nigerian] government stepped in," he added.
"The players have been assured of adequate medical care on the plane. It's been challenging but most importantly we will be ready for the first game."
Their flight is set to depart at 1200GMT for the seven-hour flight to Manaus, where their Group B opener kicks off just 13 hours later.
The squad had originally been stranded in Atlanta because of a problem that seemed to be caused by money having to go through different bank accounts and currency conversions.
"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.
"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.
One of the players explained to the BBC on Wednesday: "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.
Nigeria's Olympic football team will arrive just hours before their opening Rio 2016 match after being delayed because their plane was too small.