FIFA says it is analysing a claim from Brazilian side Santos regarding irregularities over Neymar's transfer to Barcelona two years ago.
Football's world governing body confirmed on Friday that Santos have filed a claim and said "the matter is currently pending and being investigated."
Santos claim the Brazilian player and his agents broke the terms of Neymar's contract by starting negotiations with Barcelona without the Brazilian club's consent.
If FIFA rules in Santos' favour, it could lead to sanctions against Barcelona and Neymar.
Santos confirmed they have appealed to FIFA but claim they are not trying to cause problems for their former star, only attempting to "protect their rights and seek reparation of damages."
The Brazilian club said they lodged a formal complaint in May and only released a statement on the matter now because there were reports in the Brazilian media saying that said the club were demanding the player's suspension for six months.
"Santos have not made any additional request to FIFA [demanding a suspension],'' the club said, adding that it's up to the governing body to decide on an eventual punishment for Neymar or Barcelona.
FIFA said it wouldn't comment "nor to give an estimation of the time line" of the case.
Santos claim they were never told about a 2011 payment of €10 million ($11.4m) made by Barcelona to the company owned by Neymar's father to guarantee the rights to sign the talented youngster.
Santos said that although the player was authorised to talk to clubs, nobody ever informed the Brazilian club that a deal with Barcelona was reached at the time.
Another €30m ($34.3m) was paid directly to Neymar's father's company after the deal was finalized in 2013, and Santos was paid about €17m ($19.4m).
Former Barcelona president Sandro Rosell eventually resigned amid allegations that he hid the real cost of Neymar's transfer in false contracts.
Neymar's father, Neymar da Silva, told Brazilian media on Wednesday that "Santos are going against their idol.
"We will defend Neymar against Santos if needed," Da Silva said. "It seems Santos are looking for more money."
Neymar's father has always claimed that Barcelona never broke FIFA rules that prevent teams from luring players under contract with other clubs. He said Santos knew about the deal and the money was paid to his company, not directly to Neymar.
Da Silva said that if the player had changed his mind and decided to go to another club, or if something happened to keep him from signing with Barcelona, he would have had to return the money to the Spanish club.
The deal came before Barcelona and Santos faced each other in the final of the Club World Cup in December 2011. Neymar was not a factor in the match, and Barcelona won 4-0.
The player's agent, Wagner Ribeiro, claims the entire proceeding is "absurd" and has no basis in law.
The summer 2013 transfer to Barcelona is still under investigation by the Spanish and Brazilian courts.
The star's former team have received a relatively small share of a transfer fee that was initially publicly announced as €17.1m, although the full cost of the deal has been revealed to be well over €80m as the investigation has proceeded.
The Sao Paulo-based outfit are reportedly seeking payment of €55m in damages, and the club's president, Modesto Roma, told the Esports Cope radio show on Cope Catalunya that courts on both sides of the Atlantic had ruled that the transfer had not been done correctly.
"I presented the official complaint in May," Roma said. "Despite being an idol, we will denounce Neymar because there are things we do not agree with. In the transfer, things were not done in a clear and transparent way. That is proven in the Brazilian courts and by the Spanish prosecutors. We understand the administrative discussion we must have with FIFA. There are things not done right, and FIFA must make a ruling."
Ribeiro, who advises Neymar Sr., told El Partido de las 12 that Santos' move was "unconstitutional."
He said: "Santos now wants to get the money, which belongs to his father. It is absurd. In 2011, Santos authorised Neymar to sign up with a company to manage his transfer."
The legal entanglement has led to some speculation that Neymar might cut his ties with Barcelona, and Manchester United have been mentioned as one possible future destination.
However, Ribeiro said the furor would not affect Neymar's plans to sign a new contract to remain at the Camp Nou for many years to come.
"I spoke today with Neymar's father and he has told me he is very happy at Barca, and has no hurry to renew," he said. "But you can be sure that Neymar will be at Barcelona for many years. Without any doubt."
Information from The Associated Press was used in this report.