Juncker told the Spanish newspaper El Pais on Sunday that "Catalonia is an enormous concern. I don't like the situation it has provoked, it is a disaster", AP reported.
He sent a message to Carles Puigdemont, the ex-Catalan leader who fled to Belgium, that Catalan secessionists "must not underestimate the wide support that (Spanish Prime Minister) Mariano Rajoy has throughout Europe".
Spain is facing its worst institutional crisis in nearly four decades after Catalonia's regional parliament violated the Constitution by voting to declare independence on October 27.
Rajoy responded by firing its government, dissolving its parliament and calling a regional election for December 21.
Juncker says the election "could, should improve" the situation.