LaLiga president Javier Tebas believes that Florentino Perez has had an effect on the way VAR is used in Spain.
Luis Rubiales admitted that the Real Madrid president had called him to complain about the new technology last January.
"In March, we're going to call an assembly with all the clubs and speak about VAR," Tebas told COPE and Radio MARCA.
"If we're seeing everything that is happening, we're seeing that there's a lot of unease.
"There was a before and after Florentino's call to Rubiales, this generated a problem that is still dragging on. I think that it was an error to say that Florentino had called at 20 minutes.
"There's no unification of criteria and VAR intervenes too much, but there aren't any technical problems."
Perez and Real Madrid didn't support Tebas as he was re-elected LaLiga president in December, and neither did Barcelona.
"[Luis] Rubiales asked me to step down twice, I did it and I came back to win," Tebas said.
"LaLiga is more than Barcelona and Real Madrid. They don't like that I'm president, but they work with it.
"[Perez and I] have a different concept of LaLiga. I want it to be the best competition and he wants Super Leagues or global leagues. He's asking for independence, pretty much.
"I haven't spoken to him in over two years. I spoke with [Josep Maria] Bartomeu five months or so ago."
Former Real Madrid goalkeeper Iker Casillas is set to challenge Rubiales in the Spanish Football Federation (RFEF)'s presidential elections this year.
"It all seems absurd and strange to me," Tebas said.
"I haven't spoken to Casillas since he announced this. I haven't spoken about this possibility with him.
"The last time he asked me about Spanish football, I told him that I was very worried and that I didn't agree with what the Rubiales' team is doing.