Fifa has revealed it was ready to pay Ghana's players their World Cup bonuses directly and deduct it from the Ghana Football Association's prize money.
After Ghana's players boycotted training in protest at not receiving their money, the country's government flew $3m (Â£1.8m) in cash to Brazil.
Fifa secretary general Jerome Valcke described the situation as sad.
"The players have the right to receive their money but it would be much easier to do this by bank transfer," he said.
"The fact that the money came in cash is also sad because I was ready to sign a letter, as long as I had a copy of the agreement between the national association and the players, that the money would be paid by Fifa by bank transfer into their personal accounts.
"Fifa would have made sure to deduct the players' money from the prize money paid to the national association."
While Ghana have now gone home from Brazil, having been eliminated from the tournament at the group stage, another bonus row is ongoing involving Nigeria.
The Super Eagles, who are due to meet France in the last 16 on Monday, refused to train on Thursday over fears they would not receive their bonus payments from the Nigerian Football Federation, the BBC understands.
It prompted Nigerian President Goodluck Jonathan to speak to senior players on Friday to assure them that the money will be paid.
There was a similar issue with Cameroon, whose players refused to board their plane to South America because of a row over appearance fees. They arrived for the World Cup a day later than scheduled.
The issue is not a new one - Togo went on strike over bonus money at the 2006 tournament in Germany and Fifa was forced to intervene.
And Valcke says that something needs to be done.
"Future World Cups will ask the national associations to provide us with their agreements with their players to make sure that this kind of episode does not happen again," he said.