The Nigeria Football Association, NFA, said on Tuesday in Abuja that it had paid John Obuh, the Flying Eagles' chief coach, the backlog of his monthly salary.
Obuh had earlier threatened to resign his appointment over the unpaid salaries.
The coach stayed behind as the national under-20 men's team departed for Egypt on Monday for two friendly matches ahead of a three-week training camp in Tunisia. The training camp is in preparation for the African Youth Championship (AYC) beginning in Algeria on March 16.
Musa Amadu, NFA's Secretary-General, said everything was under control as Obuh was already on his way to Egypt to join the team.
He said while the coach reacted over the salaries owed him, he did not travel with the team because of the leave of absence granted him by the association.
"I want to make it clear that there is no problem whatsoever between the NFA and coach John Obuh. He remains the coach of the under-20 team and the team is right now in Egypt.
"It's just that Obuh was given a day's leave of absence to settle certain family matters and he has done that. Of course, he is going to be away until the end of March. So, he obviously needed to settle his family before he traveled and he had done that.
"As I speak with you, Obuh is at the airport taking an Egypt Air flight to Egypt," Amadu said.
The NFA secretary-general said nothing had happened to suggest that the team or its coach was not motivated to defend the trophy Nigeria won two years ago in South Africa.
He also said the NFA had gone a step further to prepare the team for the FIFA U-20 World Cup billed for Turkey in June with its registration for the Toulon Tournament in France.
Amadu said this was to put the team on a sound footing to face countries such as Brazil, which had qualified for the World Cup.
"There is no other country that has won the AYC more than Nigeria.
"We got to the quarter-finals of the World Cup in Colombia two years ago and the project is not just for us to retain the trophy in Algeria, which we are capable of, but to excel at the World Cup.
"I am confident that, going by the camping they have undergone in Abuja for over one month and coupled with the friendly matches lined up for them against their Egyptian counterparts in Egypt, they will emerge victorious," he said.
The Flying Eagles will in Egypt play two warm-up matches against their Egyptian counterparts on February 20 and February 22.
The team will depart Egypt for Tunisia on February 23 for the final phase of camping for the AYC beginning on March 16 in Algeria.