The club has been accused of instigating the probe by a Spanish journalist, but has strongly rejected those claims.
The Spanish High Court is continuing its probe surrounding the alleged misappropriation of funds by the club's former president Sandro Rosell - who resigned last week - in securing the signing of the Brazil star.
His replacement, Josep Maria Bartomeu, has since revealed that Barca paid Neymar's parents 40 million euros of the total €57.1 million transfer fee.
This news was then followed by suggestions from a Catalan journalist, Xavi Bosch, that Madrid was responsible for sparking the investigation - claims fiercely denied by los Blancos.
A statement on the club's official website read: "Given the serious demonstrations last night by RAC 1 journalist Xavi Bosch, the president of Real Madrid Florentino Perez wants to state the following:
1. It is flatly a false assertion that aims to involve absurdly the president of Real Madrid with the judicial process initiated following the complaint filed by a member of FC Barcelona against president Sandro Rosell.
2. Real Madrid president demands that the journalist author of such misrepresentations rectify those claims in the same medium of communication clearly and immediately.
3. If this correction does not occur, the president of Real Madrid will file suit against journalist in defense of the right to honor, privacy and self-image. This has already been sent to the lawyers the content of the allegations made."
Barcelona board member Jordi Cases was the man responsible for initially raising concerns over the small print of Neymar's transfer and has refused to drop his complaint.