It wasn't clear how Ghana would bring such a large amount of cash into the country without declaring it and paying tax on it in line with Brazilian law.
World Cup prize money which ranges in Brazil from $8 million for being knocked out in the group stage to $35 million for winning the title is normally paid after the tournament.
The Ghana Football Association insisted that the problem had been resolved after intervention by Ghanaian President John Dramani Mahama, who had spoken to players and guaranteed they would get their money by Wednesday afternoon, the GFA said.
Yet FIFA hasn't yet made a decision on handing over any prize money to Ghana in advance.
The bonus row seriously disrupted Ghana's preparations for its decisive Group G game against Portugal on Thursday, although Ghana midfielder Christian Atsu dismissed fears the team would boycott its final group game in Brasilia, which the Ghanaians need to win to stand any chance of reaching the second round.
"We are not going to say we are not going to play because of the money," Atsu said. "We love our nation and we are going to play for our nation."
Ghana coach Kwesi Appiah said he had been having "sleepless nights" over the issue which came to a head Tuesday when the players and team management had a meeting instead of conducting a training session. President Mahama "personally spoke to the players" to assure them they would receive the money, the Ghana Football Association said in a statement. Ghana's players trained as scheduled Wednesday in Brasilia.
"The management and the government are trying to sort it out and everything will be sorted out in two or three hours' time," Appiah said. "They should have received it before the start of the competition but it's being solved now and we are really focused on the game now."
Players were going to receive the money in cash because "the practice in Ghana has always been paying the money in cash," Appiah said.
Asked what the players will do with the appearance fees reportedly between $75,000 and $100,000 each if they received them in cash, midfielder Atsu said: "I think we will keep it in our bags and we'll just lock them. And we will transfer the money to our accounts."
Coach Appiah wouldn't give an exact figure for the appearance fees owed to the players, saying: "I would be a bad person ... the players would kill me if I said."
Brazilian officials said bringing in $3 million in cash and not declaring it to authorities would be illegal and the entire amount could be confiscated. Individuals cannot bring in more than $4,500 each without having it subject to taxes, said Brazil's Federal Police, who enforce custom and immigration laws.