Barca are refusing to pay €26million, which was included in the contract extension he signed with the club last October, to the Brazil star and his father.
The club say that Neymar was in breach of the terms of that contract when he negotiated with Paris Saint-Germain prior to his world-record €222m transfer, meaning the clause in the deal stipulating the bonus is null and void.
Neymar's father, who also acts as his agent, accused Barca of "blackmail" in their refusal to pay and FIFA is now looking into the matter.
A spokesperson from world football's governing body told Omnisport: "The matter ... is pending and being investigated. As a result, we are not in a position to comment on it."
Barca spokesperson Jordi Vives has previously stated: "There were three conditions [to the loyalty bonus]: one, that the player does not negotiate with another club in the last three months before July 31.
"Two, that he will express publicly his commitment to fulfil his contract.
"Three, the collection was to be made on September 1, to ensure that he did not go to another club.
"Now that we know that none of these three conditions were met, we will not honour that bonus."
The complaint is a separate case to Barca's lawsuit against Neymar, which was announced on Tuesday.
The Catalans are suing the 25-year-old for an alleged breach of contract in the wake of his PSG move, demanding he pay back a bonus he was given for signing his new contract last year, as well as €8.5m in damages and an additional 10 per cent in arrears.
Photo Getty Images. Caption: Paris Saint-Germain forward Neymar