The weekly cabinet meeting usually takes place in Madrid but Prime Minister Pedro Sanchez's Socialist government decided to hold it in the Catalan capital, igniting protests.
Catalan President Carles Puigdemont and Spanish Prime Minister Mariano Rajoy exchanged letters on Monday but made no headway in the dispute. Madrid has now given the region until Thursday to clarify whether it wants independence.
Spain's central government has sent about 10,000 extra police officers to Catalonia for the referendum.
Authorities are looking for 22-year-old Younes Abouyaaqoub, who they believe was behind the wheel of a van which left a trail of dead and injured on Barcelona's famed boulevard.
A missing imam, a van driver and a house that exploded days ago have become the focus of the investigation into an extremist cell responsible for two deadly attacks in Barcelona and a nearby resort.
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