Joan Laporta claimed Real Madrid have always been favoured by referees as he labelled the capital club "the team of the regime".
Barca's president spoke at a press conference on Monday to robustly defend the club amid allegations they made payments to Jose Maria Enriquez Negreira, the former vice-president of the technical committee of referees.
The club are subject to a UEFA investigation with prosecutors in Spain pursuing charges for alleged corruption. Barca are accused of having paid over €7million to a company owned by Negreira.
Laporta, though, has insisted Barca have no case to answer, as he looked to turn the spotlight onto rivals Madrid.
"I want to mention a club which decided, on its own, to appear in court when the trial happens," Laporta said.
"A club saying that they feel wronged. A club, Real Madrid, which has historically been favoured by arbitration decisions. Historically and currently. A team that has been considered the team of the regime of the day due to its proximity to the power of the day.
"They were the team of the system because they were close to the political and financial power. I think it's worth mentioning that for seven decades the big majority of the presidents of the technical committee of referees have been former members or players of Real Madrid.
"For 70 years the people who assigned the referees were former members or former Real Madrid players. In some cases, all of those at the same time.
"For this club to appear in trial and say they feel wronged for the best period in Barcelona's history, this trial will be used to take their masks off. It's an unprecedented exercise of impudence."
Laporta, who said the allegations represented "one of the most ferocious attacks in our history" reiterated Barca's innocence.
"Throughout our 123-year history, Barcelona has always been a model of fair play, both on and off the field," he said.
"If we have won for so many decades, it has undoubtedly been a result of effort, talent and knowledge.
"No campaign to discredit us will prevent us from continuing to be an organisation of reference in the world of sports that is beloved and admired by millions of Catalans and by many more millions of people around the world.
"I am fully convinced that Barcelona has never performed any act with the intention of altering the competition to gain an advantage.
"If there were any person or private entity outside Barcelona that had taken advantage of this context to commit irregularities, the club would be the first to fully investigate. Our image is at stake.
"Accusations must be proven. We live by the rule of law, which guarantees among its basic principles the presumption of innocence. I reiterate with all my resolve, I am convinced that Barcelona has not committed any crime of sports-related corruption. I hope that sooner rather than later, the club is fully exonerated.
"Consulting on technical-refereeing issues does not constitute any type of illegal act. Consulting – as is done by the big clubs – that was carried out transparently, with the corresponding invoices, at least in my first mandate as president."
Barca were held to a 0-0 draw by Getafe on Sunday, though they hold an 11-point lead at the top of LaLiga with nine games remaining.