According to Spanish newspaper AS, a petition was raised against the club, former president Sandro Rosell and current incumbent Josep Maria Bartomeu.
The acquisition of Neymar has been under the spotlight over the past 12 months after his move from Santos prior to the 2013-14 campaign, a deal estimated to be worth in the region of €57 million although some claims suggested it was closer to €95m.
The furore led to Rosell leaving his post and Bartomeu stepping up in his place, and he has continued to claim the transfer was completed with all the relevant documentation.
Following the claims on Tuesday, the Catalan giants have hit out and expressed their "indignation".
"Barcelona has declared its innocence, and provided all of the documentation requested on numerous occasions," a statement read.
"It is Barcelona's wish for the judge hearing this case to reject the requests being made by the Prosecutors Office, as all of the actions involved in the player's transfer process were conducted with no intent whatsoever to breach the law in any way.
"Barcelona shall not allow any action to tarnish the club's image or to damage or dishonour what it considers to be a historic and strategic signing."
Barca went on to vehemently deny any wrongdoings by Bartomeu, providing an explanation for the tax offence brought against him.
They added: "In this [Bartomeu] case, the charge is related to a payment of five million euros, the final part of the 40 million that the club was obliged to pay to the N&N company for the transfer of the player, and which it was stipulated would be paid on 31 January 2014, eight days after the change of president.
"The decision to defer this payment to January 2014 and the discussion about the type of tax retentions that should be applied to the same, do not seem to be sufficient grounds to press charges.
"Moreover, the complementary statement presented as a precautionary and preventative measure in February 2014 already covered any interpretations that could be made with regard to the retention to be applied to this payment."
