Speaking in the Catalan coastal town of Sitges, Rajoy told the Circulo de Economia business group that if Catalonia breaks away from Spain it could lose up to 30 per cent of its GDP and would have to seek readmission to the European Union.
Catalonia, whose capital is Barcelona, represents a fifth of Spain's GDP and has a population of over seven million.
Rajoy compared the campaign for the referendum on independence to the recent vote in Britain to leave the EU.
Rajoy repeated his pledge that his government won't permit the referendum, which he has called unconstitutional. "I am not going to authorize a referendum on independence because I don't want to and because I cannot do so," Rajoy said.
More From This Section
The Catalan government has said it will hold the vote anyway by September.
The president of the Circulo de Economia, Juan Jose Bruguera, urged Rajoy to resolve the political conflict by finding "alternative means that are not just black and white."