Reports emerging from Catalan radio station RAC1 on Monday claimed that Perez may have been behind Barca member Jordi Cases' requests for the €57.1 million move to be investigated.
It has since emerged that €40m of the fee was in fact paid to an agency owned by Neymar's parents, with the forward's former club Santos seeing little of the sum total.
Barca president Sandro Rosell stepped down from his role last week, citing threats against himself and his family in the midst of the row as a key factor.
But Perez has denied any involvement in the controversy, and has threatened legal action in a bid to clear his name.
A club statement read: "In the light of the serious allegations made last night on RAC 1 by the journalist Xavi Bosch, the president of Real Madrid, Florentino Perez, wishes to make the following statement:
1. The allegations are totally false and they absurdly try to involve the president of Real Madrid in the legal proceedings started by a member of FC Barcelona against the club’s then president, Sandro Rosell.
2. The president of Real Madrid demands that the journalist who made these false allegations issue a clear and immediate rectification on the same radio station.
3. If this rectification is not made, the president of Real Madrid will sue this journalist in order to protect his honour, his privacy and his reputation. To this end, he has instructed his lawyers to study the content of these allegations."
