The team finally agreed to train in Alexandria, 30 minutes after schedule, after the Nigerian Football Federation (NFF) promised to pay a win bonus from their 1-0 victory over Burundi on Saturday, by the end of the week.
NFF spokesman Ademola Olajire told AFP "the matter has been resolved", conceding that funds for the tournament had arrived late.
"The NFF received part of the money meant for the tournament today and is in the process of converting it to dollars to pay the players and officials", he said.
"The only money they’re owed is the win-bonus for the Burundi match", he added.
The bonuses were expected to be paid by the NFF after Saturday's game ended.
Officials close to the team, who spoke under anonymity, told AFP that following reassurances from the NFF "the team captain spoke to the players, asking them to show some understanding after which the team agreed to train".
The players had earlier boycotted the official pre-match conference.
Other NFF officials disclosed that the players have been paid a daily training allowance of $200-a-player from June 2 to June 30.
Nigeria's top football body -- cash strapped and besieged by corruption trials against its top officials -- have struggled to pay athletes their bonuses and allowances at several tournaments.
Both the women's senior team at the Women’s World Cup in France and the men's FIFA U20 World Cup team in Poland also embarked on pay strikes to press for their entitlements.