It comes with Spanish prosecutors requesting a prison sentence of two years and three months for Barcelona president Josep Maria Bartomeu and seven for his predecessor, Sandro Rosell, over the so-called Neymar affair.
The two men and the club are charged with tax fraud and Rosell is also accused of accounting irregularities over his time in charge.
The Madrid court is also calling for a fine of 22.2 million euros ($24.1 million) against the club over the transfer deal, which has been the subject of an anti-corruption probe.
“I am convinced the people involved in this process proceeded at all times respecting the laws of Brazil and Spain while also respecting statutes of (world governing body) FIFA,” Neymar da Silva Santos said in a statement.
Prosecutors say Neymar’s transfer cost in 2013 was “at least 83,371,000 euros” and not the 57 million initially reported by Barcelona.
Neymar senior did not mention Rosell or Bartomeu in his statement, but said he wanted to stress that neither he nor any of his partners were the subject of investigations, “contrary to what some Brazilian media have intimated in recent days.”
Following months of investigation, a Spanish judge must now consider whether the case should go to trial.