A telephone call between FIFA general secretary Jerome Valcke and an unnamed Nigerian official broke the impasse after the 23-man squad refused to travel to the tournament in a strike action designed to force the hand of their federation.
"I've spoken with the team manager and they will be in the plane on Saturday and they will arrive for the Confederations Cup. The problem is solved," Valcke told a news conference in Rio de Janeiro, when asked about the problem.
Nigeria's squad were supposed to leave Windhoek, one day after drawing 1-1 with hosts Namibia in a World Cup qualifier, for Johannesburg to connect with a flight to Brazil, where they are representing Africa at the eight-team, two-week tournament.
But the players refused to leave the hotel in a row over promised payments for points garnered in two World Cup qualifiers against Kenya and Namibia over the last week.
Bonuses had been cut in half from $10,000 to $5,000 by the Nigerian Football Federation, local sources said, in what was presented as a cost-cutting measure but the players refused to accept new terms and decided to strike.
"They are declining to leave," Namibia FA general secretary Barry Rukoro told Reuters earlier on Thursday.
"They were supposed to go at 11 a.m. this morning but they say they are owed money by their association and want it sorted before they will leave the hotel.
"Their officials all departed on an earlier flight this morning but the players and the technical staff are still here."
Nigeria are due to play their first game in the tournament against Tahiti in Belo Horizonte on Monday but will have little time to acclimatise to the conditions.
It is the second major controversy to rock Nigeria since they won the African Nations Cup in South Africa in February.
Coach Stephen Keshi resigned the day after they won the title, telling South African radio station Metro FM there were continual efforts by unnamed officials to undermine his work.
However, he was persuaded to quickly change his mind in a tawdry affair that took some of the gloss off Nigeria's triumph.
Striker actions are nothing new in Africa and are used as a tactic by players desperate to secure promised payments.
- Sports & Recreation
- Jerome Valcke