Abdullah Ghubn, who runs the Andalusian club on behalf of Qatari owner Sheikh Abdullah al Thani, said Barca and Real should agree a fairer distribution of TV cash to help level the playing field in Spain's top division.
Football's two richest clubs by revenue take around half the annual pot of 600 million euros (£527 million) for La Liga rights, giving them spending power to afford the transfer fees and wages commanded by the best players.
"Today people will be excited to see a 'Clasico' (Barca v Real game), next year the same but in a few years people will get bored of this because this is a league of two clubs," Ghubn told Reuters in an interview at Malaga's La Rosaleda stadium.
"So they will lose and tomorrow the audience will come down and some other league will be trying to rise up," he added.
"They will have less money from TV rights. They have to realise if they will not share the cake they will not get the cream."
Barca and Real, who again finished the season out of sight at the top of the standings, negotiated their current TV deals individually, unlike in England and rival European leagues where clubs bargain collectively and income is shared more equitably.
An agreement the two giants brokered late last year with 11 other top-flight sides on sharing some of the TV cash from 2015 is likely to cement their advantage while helping the others only marginally, analysts have said.
Malaga, who do not rely on TV money thanks to the sheikh's investment, was one of the club's who did not sign up and Ghubn said they had opted out because the accord set unacceptable limits on the smaller clubs.
Perched on a white armchair in the club's corporate suite, the Libya-born 31-year-old, who is of Jordanian nationality, suggested Spain's football authorities needed to step in to enforce a fairer distribution.
"I don't think we'll see a solution soon to this issue because nobody can handle it," he said. "If you have someone who can handle this and act as a judge, a person who could say how things should be it would be much better."
Malaga, who were struggling financially before Sheikh al Thani stepped in, narrowly avoided relegation in the campaign just ended.
A number of new arrivals in the January transfer window, including Brazil forward Julio Baptista, helped preserve their top-flight status and Ghubn said the club were aiming to qualify for Europe next season, when they will have a budget of around 100 million euros.
The former Manchester United and Real Madrid player spoke at a club event at the city's Picasso Museum on Wednesday, marking the signing of Malaga's partnership with UNESCO, the United Nations Educational, Scientific and Cultural Organisation.
"We are confident we can reach our goals because we know exactly how we can be strong and what we are missing," Ghubn said.
"We have no limited budget. You have to look for the right players to suit your project so you cannot be very specific on how much you have to spend."
"The media was mentioning 120 names so I don't think we can go for 120," Ghubn said.
"Pastore is a good player, he's a very good player and he's a target for any club.
"We have many options. But this year we are going to have good players we are looking for specifically according to our system.
"We have a plan to do something very big and very huge so our dream is not limited to one level.
"We have an agenda, we have a philosophy, we have time to do something very special for this club."