Cameroon's squad refused to board a plane to Brazil on Sunday until the issue was resolved, and eventually left for the tournament 12 hours later than scheduled.
CFF spokesperson Laurence Fotso revealed the governing body was forced to secure a private loan against future FIFA World Cup payments.
"Everything is ok now," said Fotso. "That money is given (by FIFA) three months after the end of the competition, so we borrowed money as a private loan to satisfy the players."
Cameroon coach Volker Finke had played down the situation prior to the team's departure, suggesting the row was "not really as big as people made it out to be".
Neither the bonus dispute, nor the absence of talismanic striker Samuel Eto'o, affected Cameroon in their final warm-up match in Yaounde on Saturday as they beat Moldova 1-0.
Finke's men begin their World Cup campaign with a game against Mexico on Friday.
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