The president of the Spanish Football League (LFP) Javier Tebas says Barcelona and Catalan rivals Espanyol would not be admitted to La Liga if Catalonia becomes an independent state.
A referendum on Catalan independence has been called for November 9, but the Spanish government are attempting to block it.
Speaking at a press conference, Tebas stated: "Barcelona and Espanyol would not play in La Liga if Catalonia gains independence.
"I cannot imagine a Spain without Catalonia nor La Liga without Messi," he added.
Tebas believes Spanish law would prevent the two clubs from operating in the national league.
The president of Spain's Catalonia region, Artur Mas, signed a decree on calling an independence referendum on November 9.
The central government has said the vote would violate the constitution and has promised to block it.
Spain's Prime Minister Mariano Rajoy has called an special cabinet meeting to challenge the vote in the constitutional court.
Hundreds of thousands of protesters in Spain) human chain today to make their demands for independence heard.
Demonstrators wore yellow T-shirts and draped themselves in blue, red and yellow separatist banners as they joined hands through cities and along rural roads.
Many Catalans feel their region has been treated unfairly over taxes and cultural issues such as the Catalan language, despite having significant self-governing powers.
Polls show backing for secession has risen steadily in Catalonia, with some registering support as high as 50 percent.
The pain of recession in Spain has persuaded the people of its Catalan region to edge ever closer to independence.
Elections for its local Parliament gave almost two-thirds of the seats to parties who want a referendum on breaking away.
Catalonia in northeastern Spain has a population of 7.5 million and includes Barcelona, Spain's second biggest city.
Catalonia also produces 20 percent of Spain's GDP and its economy matches Portugal's.
From Barcelona, our Europe Editor James Mates reports.