The Catalan club are under investigation for fraud following alleged failure to declare €37.9 million (£31.2m) relating to the Brazilian's transfer between 2011 and 2013
In a document submitted on Wednesday, prosecutors claim Barca failed to pay a sum of €9.1 million (£7.5m) owed on a taxable payment of €37.9m (£31.2m).
A complaint by Barca socio Jordi Cases over 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 press conference later that week that broke down the costs of the transfer.
Those revealed that Barcelona had in fact paid out €86.2m (£71m) in the total cost of the operation, although the Catalan club insisted that the transfer itself remained at the oft-quoted figure of €57.1m (£47m).
It also emerged that the Blaugrana had paid €40m (£32.9m) 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 offences between 2011 and 2013, relating to the signing of Neymar.
Barca have yet to respond to the latest allegations.