The comments followed earlier reports that players were demanding unpaid bonuses and that a training session on Thursday had been canceled because of the dispute. (Agencies)
However, media officer Ben Alaiya told reporters: "It is settled now. It's absolutely settled now. Let's not dwell on the past. There is no problem now and that is why everyone is training."
Alaiya said Thursday's training had been canceled because a team meeting near its base in Campinas, north of Sao Paulo, had overrun leaving no time for the session.
"We never had problems with money," Alaiya said.
"Everybody is paid what they are due, up to date. There are no bonuses owed to the national team of Nigeria,” he added.
The African champions flew to the capital Brasilia on Friday ahead of the knockout game against the French on Monday.
Nigeria is not the only African team to have had problems with player payments.
Fellow West African teams Cameroon and Ghana have both had their World Cup campaigns badly distracted by pay disputes.
Cameroon's squad refused to get on a plane to Brazil at the beginning of the month until their bonuses were improved and Ghana said it flew in cash from back home to keep its players happy ahead of the decisive final group game against Portugal.
Both Cameroon and Ghana were eliminated in the group stage.
Last year, Nigeria arrived days late for the Confederations Cup in Brazil because of a row over player payments, which resulted in the squad refusing to leave a hotel and travel for the World Cup warm-up tournament.
The problems also re-surfaced earlier this month at the World Cup and a Nigerian politician visited the team camp in Campinas to mediate between players and federation officials.
The Nigeria Football Federation then announced two weeks ago that the bonus structure had been agreed upon with players getting USD 10,000 for every game they win in the group stage.
The bonuses will improve with victories in the knockout stages. Each player would get an additional USD 12,500 for beating France in the last 16.
Nigeria's team meeting on Thursday came just hours after the NFF released a statement, saying there were no problems in the squad over bonuses.
"We understand that some people are playing politics but they must leave us out of it so that we can do well here and go far in the tournament," coach Stephen Keshi was quoted as saying in the statement.
Nigeria qualified second behind Argentina in Group F, making the second round of the World Cup for the first time since 1998.
The comments followed earlier reports that players were demanding unpaid bonuses and that a training session on Thursday had been canceled because of the dispute.