A total of 465 people were attended to at hospitals and health centres, a spokeswoman for the Catalan government's health department said. So far 92 have been confirmed as injured, two of them seriously.
One of those seriously injured has an eye injury while the other suffered a heart attack during a police operation in Lerida, about 150 kilometres (95 miles) west of Barcelona.
Spain's interior ministry said 12 police officers had been injured in the clashes.
Hundreds of people had gathered before dawn at the polling stations set up in schools and other public buildings for the referendum which Spain's central government and the court have ruled is unconstitutional.
Spain will answer to international courts - Catalonia spokesman
Catalonia's government spokesman Jordi Turull said the Spanish government will answer to international courts over the violence by police.
"The Spanish state has been very compromised and will end up responding to the international courts," he said during a press conference.
Turull said he believed millions of votes would be counted and, while the voting hours wouldn't be extended, those already queuing to cast their ballot would be allowed to do so.
He said he did not know when the vote count would be finalised.
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