Los Blancos were two points behind Barca when the competition resumed in mid-June, but are now four clear at the top of the table with four rounds remaining.
Madrid have won their last two matches 1-0 thanks to late penalties and have had marginal decisions go their way in the victories over Eibar, Valencia and Real Sociedad.
"I watched up until the end of the second half [of Real Madrid's win over Athletic Club] in Bilbao," Bartomeu told Movistar+ on Sunday night.
"It was another victory for Madrid and I will repeat the message: it leaves a bad taste for me because it is the best league in the world and VAR is not up to standard. That is impacting on some results.
"It seems to always favour one team. Even though some results of ours that have not been good, VAR has not been equitable and there are teams that have been hurt."
Bartomeu revealed that he had taken up the matter with the Spanish Football Federation.
"We have spoken to the RFEF and VAR should help the referee," he said. "We've all seen a lot of images and plays where it hasn't been equitable."