According to a judge at the Spanish High Court, the Catalan club failed to declare a €37.9 million (£31.1m) payment in their signing of the Brazilian forward from Santos
The Catalan club were hit with news of the latest probe on Wednesday as prosecutors claimed Barca failed to pay a sum of €9.1 million (£7.5m) owed on a taxable payment of €37.9m (£31.1m), and despite pleading their innocence in a statement released on their website, judge Pablo Ruz revealed on Thursday that the Blaugrana will be charged in court.
The charges concern alleged fiscal irregularities between 2011 and 2013, relating to the Brazilian's controversial transfer.
In a document submitted on Wednesday, prosecutors claimed Barca failed to pay a sum of €9.1m owed on a taxable payment of €37.9m to the player's parents, with the judge considering that Neymar - as a non-Spanish resident - would be obliged to pay tax on that sum in either Brazil or Spain.
"We express our total willingness to collaborate with the Justice authorities in this matter, as we have done since the first moment the issue arose and in any other area in which our presence may be required," Barca's statement read on Wednesday.
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 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).
Bartomeu has vowed to fight all charges in the controversial case.