"We can confirm that we received a claim from the club Santos concerning the player Neymar and the club FC Barcelona," FIFA said in a statement to Reuters.
"The matter is currently pending and being investigated."
Santos president Modesto Roma announced in May that he intended to take the case to FIFA over an alleged breach of contract.
The club issued a statement on Thursday confirming the move, but denied Brazilian media reports that they had asked for Neymar to be banned for six months.
"Santos have not made any additional request to FIFA, the procedure is underway as requested initially," said the club.
"Santos are only trying to protect our rights and obtain compensation for the damages we have suffered."
(Writing by Brian Homewood in Berne; editing by Toby Davis)
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