Judge Pablo Ruz said in his decision, released in Madrid today, there was enough evidence to merit charges over Neymar's 57 million euro (then £47m) move from Santos last summer.
Ruz is also investigating former Barcelona president Sandro Rosell over the deal.
Rosell quit soon after it emerged 40 million euros (£33m) of the transfer was paid to a firm operated by Neymar's father, who has been called on to testify by Ruz.
The decision comes a day after public prosecutor Jose Perals charged Barcelona with fabricating simulated contracts and using "financial engineering" to defraud the Spanish Treasury.
Barcelona have denied the charges.