The club has issued a statement declaring its "utmost indignation" after a High Court prosecutor said on Friday that the written documents for the player's move were misleading.
An investigation into the Blaugrana's 57 million euro deal for the Brazilian during the summer is seeking to establish where a €40m payment - which didn't end up in the hands of Santos - ended up.
Jose Perals stated on Friday that "the contracts signed may have been faked in order to alter the concept of the payments" and could call on Barca auditors to provide evidence of the transaction.
Barcelona has always maintained that there was no impropriety on the part of the club or president Sandro Rosell in the deal, and has since issued a statement in defense of the transfer.
"Barcelona wishes to express its utmost indignation at the report from the prosecutor of the High Court on the signing of Neymar released on Friday," the statement on the club's official website reads.
"It is unlikely that the prosecutor, after having requested the contract with the player and the club's accounts, have now called for further measures without seeking a statement from the defendant.
"It is also difficult to understand why, in their proceedings, the prosecutor requested through the offices of places like FIFA the letters which FCB has already made available to the court or could provide if required to do so, as they did on December 26.
"The prosecutor's decision casts doubt on a flawless operation which allowed FCB, for €57 million, to sign a player wanted by our competitors.
"It is questionable, moreover, that new measures are being unnecessarily undertaken in order to lengthen a process which we have always considered unfounded and reckless.
"The operation to sign Neymar was complex. We are aware of this, as we have expressed every time we have referred to the confidential nature of some of our agreements.
"That was the way to acquire the player. Our competitors were willing to do the same for much more money, but we had confidence in the expertise of our negotiating team.
"This contractual complexity, described by the prosecutor in his report as "contractual simulation" never in itself constitutes a crime. We believe the report makes a mistake in deeming otherwise.
"Given the seriousness of these facts, and despite trusting the good actions of the court, we must forcefully act in defense of the honor of FCB and its president."