Pedro Lopez Jimenez has dismissed suggestions the capital club filed a complaint against their rivals to start off an investigation which led to their year-long embargo
The reigning Spanish champions were sanctioned by world football's governing body over the breach of regulations relating to the acquisition and registration of foreign players under the age of 18.
On Thursday, Barca president Josep Bartomeu revealed Fifa opened an investigation into the Catalans' transfer policy for youth players after an "anonymous complaint" from an "unnamed club", fuelling speculation Madrid were somehow involved in the sanction.
Nevertheless, Jimenez has made it clear the Santiago Bernabeu outfit are not behind their arch-rivals' sanction.
"Neither Real Madrid, nor myself as a member of Fifa, have anything to do with the sanction that's been handed to Barcelona," Jimenez told AS.
"My membership of the Players' Status Committee is unrelated to Florentino Perez and Madrid. My appointment was a proposal of the European Club Association (ECA), of which Barcelona are members, too.
"In neither of the two meetings that I attended did we discuss a sanction for Barcelona.
"I want to make it clear that the Players' Status Committee does not have the power to hand out any sanctions. All we do is study the documents that we receive. I have nothing to do with Barcelona's sanction."
Barcelona announced on Thursday they will appeal their ban.