The Catalan club is under investigation for fraud following alleged failure to declare 37.9 million euro relating to the Brazilian's transfer between 2011 and 2013.
A complaint by Barca socio Jordi Cases about the lack of transparency in the controversial deal led to an initial investigation into club president Sandro Rosell and saw the 49-year-old tender his resignation last month.
New president Josep Maria Bartomeu then presented documents at a news conference later that week that broke down the costs of the transfer.
Those revealed that Barcelona had in fact paid out 86.2 million euro in the total cost of the operation, although the Catalan club insisted that the transfer itself remained at the oft-quoted figure of 57.1 million euro.
It also emerged that the Blaugrana had paid 40 million euro of that fee to the player's parents, but did not detail monies for third-party investors, with supermarket chain DIS unhappy at being cut out of the deal.
Bartomeu has vowed to fight any charges, but the Barca president will now be hit by this new investigation, with the Spanish High Court reguesting that Judge Pablo Ruz press charges against the Catalan club for alleged fiscal offenses between 2011 and 2013, relating to the signing of Neymar.
In a document submitted Wednesday, prosecutors claim Barca failed to pay a sum of 9.1 million euro owed on a taxable payment of 37.9 million euro.
Barca has yet to respond to the latest allegations.