Pope Francis urged Europeans not to fear unity and to put aside nationalistic and other self-interests.
Francis did not mention the police violence during Catalonia's independence referendum today on his visit to Bologna in Italy.
But in a speech to university students, Francis recalled that the European Union was borne out of the ashes of war to guarantee peace.
He warned that conflicts and other interests were now threatening those founding ideals.
Francis said: "Don't be afraid of unity! May special interests and nationalism not render the courageous dreams of the founders of the European Union in vain."
The Vatican has indicated it does not support the independence effort in Catalonia, denying a Catalan cleric's claim earlier that it would immediately recognise an independent Catalonia.
Spain's bishops have urged dialogue in the dispute.