The team was delayed last week in Atlanta, with one official saying it was because they tried to buy plane tickets to Rio de Janeiro at the last minute and then found a charter plane was too small to carry the entire delegation.
They eventually all made it onto a chartered Delta Air Lines jet, arriving in the northern Brazilian city of Manaus about six hours before their first game at the Olympics against Japan on Thursday. Despite the issues, Nigeria won that game 5-4, and then beat Sweden 1-0 on Sunday to become the first team into the quarterfinals.
Sports minister Solomon Dalung took responsibility for what he called the "unfortunate incident" and said in a statement that he went into the team's dressing room after the Sweden game to apologize to players. He didn't give details on how the mess-up occurred.
"I want to assure you that we appreciate your efforts, and I want to say that it's when a man faces challenges that his true ability is tested," Dalung said. "I am sure we all have learnt our lessons and will take the lessons to heart going forward."
Delta said a "communications mix-up" had grounded an earlier flight the team was meant to take, but there were reports that the problem was because the Nigerian government hadn't paid for the original charter.
Nigeria's soccer team is regularly beset by problems, often involving money.
A dispute over bonus payments for players at the 2014 World Cup in Brazil led to them refusing to attend a training session and almost caused the Nigerian team to go on strike midway through the tournament. The team also arrived late for the 2013 Confederations Cup in Brazil — a World Cup warmup tournament — after problems over player payments.
Nigeria and Chelsea midfielder John Obi Mikel recently denied reports that he gave $30,000 of his own money to some of his teammates on the Olympic team as an incentive.