The judge leading the judicial investigation, Carmen Lamela, also summoned the leaders of two prominent Catalan pro-independence civil groups: Jordi Cuixart of Omnium Cultural and Jordi Sanchez of the Catalan National Assembly (ANC).
Spanish Prime Minister Mariano Rajoy was unmoved by global media condemnation, denying a referendum had taken place despite more than two million ballots being cast.
During an interview with the BBC, Catalonia's secessionist leader Carles Puigdemont announced that the region will declare independence "in a matter of days".
Thirty-five people were lightly injured, while three others were "more seriously" hurt, they said on Twitter, adding that nine had to be taken to health centres. Madrid has warned it could suspend autonomy of the wealthy north-eastern region.
Some police officers were seen firing rubber bullets, storming into polling stations and pulling women by their hair.
The European Parliament will hold a special debate on Wednesday on the issue. Voter turnout was nearly 43 percent. Analysts, however, are less optimistic saying Madrid will likely suspend the government or the autonomy of the Catalan state. He also appealed for worldwide mediation to help solve the growing crisis.
In a rare intervention by the monarch, Felipe said the "irresponsible behavior" of the Catalan leaders had undermined social harmony in the region.
The European Commission went on to say that "If a referendum were to be organized in line with the Spanish constitution, it would mean that the territory leaving would find itself outside of the European Union".
The bloc urged both sides to avoid confrontation in favour of dialogue.
King Felipe accuses Catalan authorities of fracturing Spanish solidarity - video Any chance of some last-minute mediation?
Amnesty International says its observers witnessed "excessive use of force" by Spanish police.
Protesters who want Catalonia to separate from Spain march during a demonstration Monday in Barcelona.
Large crowds of independence supporters gathered in the center of the regional capital Barcelona on Sunday evening, waving flags and singing the Catalan anthem.
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