Spain is facing its worst institutional crisis in nearly four decades after Catalonia's regional parliament violated the Spanish Constitution by voting to declare independence October 27.
Prime Minister Mariano Rajoy responded by firing its government, dissolving the Catalan parliament and calling a regional election for December 21.
"Catalonia is an enormous concern," European Commission President Jean-Claude Juncker told the Spanish newspaper El Pais.
"I don't like the situation it has provoked. It is a disaster in several ways. It has charged the political atmosphere, it has fractured Spanish and Catalan society, it has caused problems inside families, between friends. It's sad."
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The threat to shatter the EU's fifth-largest economy comes while the 28-nation bloc is handling its divorce with Britain and the impact it will have on the continent's economy and fragile common political project.
"I am in favor of a Europe of regions, of respecting their identity, of what makes them different," he said.
"But that does not mean that we are going to support these regions in all their adventures, which sometimes are a tremendous error, and even more so if one declares independence unilaterally based on a referendum that lacked in guarantees."
The ballot had been banned by Spain's top court, was boycotted by parties opposed to independence, and failed to meet international standards.
Less than half the electorate participated in the poll, which the separatists won in a landslide despite violent police raids. Spain's government has defended the police response, saying it was proportionate to the aggression officers met.
"The (Spanish) government and the (Catalan government) can argue about the degree of its self-rule, but Europe is a club of nations, and I cannot accept that regions go against the nations. Especially when they are outside the law," Juncker said.
Polls forecast a tight race for the December vote between parties in favor of secession and those who want Catalonia to remain a part of Spain.
Juncker said that Catalonia's election next month "could, should improve" the situation.