The Mayor of the regional capital Barcelona Ada Colau issued a statement demanding "an immediate end to police charges against the defenceless population".
Madrid said its police had acted in a proportionate manner.
Police broke down doors to force entry into voting stations as Catalans shouted "Out with the occupying forces!" and sang the anthem of the wealthy northeastern region.
In one incident in Barcelona, police fired rubber bullets. Officers in riot gear hit people with batons and forcibly removed would-be voters, including women and the elderly, from polling stations.
Catalonian independence vote would not hurt Spain's rating
Catalan officials said over 460 people had been injured in the police crackdown and the Spanish Interior Ministry said 12 police had been hurt.
Central government's representative in Catalonia Enric Millo, referring to police action, told a news conference: "We have been made to do something we didn't want to do."
The referendum, declared illegal by Spain's central government, has thrown the country into its worst constitutional crisis in decades and deepened a centuries-old rift between Madrid and Barcelona.
It remained unclear what action the Catalan government might take.
However much voting takes place, a ‘yes’ result is likely, given that most of those who support independence are expected to cast ballots while most of those against it are not.
Despite the police action, hundreds-strong queues of people formed in cities and villages throughout the region to cast their votes.
At one Barcelona polling station, elderly people and those with children entered first.
Catalan independence referendum 'not possible' - Spanish PM
"I'm so pleased because despite all the hurdles they've put up, I've managed to vote," said Teresa, a 72-year-old pensioner in Barcelona who had stood in line for six hours.
The ballot will have no legal status as it has been blocked by Spain's Constitutional Court and Madrid for being at odds with the 1978 constitution.
A minority of around 40 per cent of Catalans support independence, polls show, although a majority want to hold a referendum on the issue.
The region of 7.5 million people has an economy larger than that of Portugal.
Differences were apparent in the conduct of the national Civil Guard and the regional police, Mossos.
In Catalonia's pro-independence heartland north of Barcelona, the Catalan force made little attempt to remove people from polling stations.
Organisers had asked voters to turn out before dawn, hoping for large crowds to be the world's first image of voting day.
Stations raided
Around 70 polling stations had been raided by police, Spanish Interior Minister Juan Ignacio Zoido said.
The aim of the raids was to seize referendum material and not to target people wanting to vote, another senior government official said.
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