The investigation is a separate complaint following Tuesday's announcement by the Catalan club that they are to sue the Brazilian for £7.8m over an alleged breach of contract in the wake of his £198m move to Paris Saint-Germain.
Barcelona are refusing to pay a £23m bonus to Neymar's father following a contract renewal last year.
A source in Spain close to the player told us earlier this month that Neymar feels "very bad" over the withheld payment.
A FIFA spokesperson has told Sky Sports News: "The matter is pending and being investigated. As a result, we are not in a position to comment on it."
Barcelona spokesman Josep Vives previously said: "The club will not pay the bonus to Neymar's father.
"There were three conditions: the player must not negotiate his departure from the club during the month before the bonus became payable, he must demonstrate his desire to fulfil his contract, and that we would not pay out the bonus before September 1, to ensure the transfer window was closed.
"Now that we know that none of these three conditions were met, we will not honour that bonus."