The referendum, declared illegal by Spain's central government, has thrown the country into its worst constitutional crisis in decades and raised fears of street violence as a test of will between Madrid and Barcelona plays out.
Chaos broke out on the streets as armed officers began to fire what appered to be rubber bullets in and around the crowds.
Witnesses said police began hitting protesters with batons, sparking a violent clash in Barcelona.
Spanish riot police were deployed shortly before polling stations opened, according to El Pais newspaper.
Elderly men and women have been carried by officers away from the voting stations, with images of bloodied pensioners appearing online.
A video on El Pais website showed helmeted riot police in a standoff with a group of angry voters near a voting station at a Barcelona school. Voters raised their hands and shouted "out".
Human chains have now been formed around the polling stations and sit-ins staged by defiant Catalans.
The National Police were deployed after the Catalan regional police did not close polling stations in line with a court order.
Spain’s interior ministry says national police and the Civil Guard have begun to seize ballot boxes and voting papers.
Spanish Civil Guard police in riot gear burst into a polling station minutes before Catalan regional leader Carles Puigdemont was due to vote in a referendum on Catalan independence from Spain that has been declared illegal by Madrid.
Police used axes to smash a window at the sports centre being used as a voting centre and forced open the door in the province of Girona.
Live TV pictures showed police with black berets and riot shields fanning out through the voting station, apparently searching for ballot boxes, while would-be voters, fists raised in the air, defiantly sang the Catalan anthem.
Mr Puigdemont had announced he would vote at the polling station near Girona at 9.30am, around the same time as the police entered, but there was no sign of him in the television footage.
He was later filmed voting.
The aim of the National Police and Civil Guard police was to seize election materials - they were not targeting people wanting to vote, Enric Millo, the Madrid government's representative in Catalonia, told a news conference.
"We have been made to do something we didn't want to do," he said.
Catalan Government spokesman Jordi Turull, spokesman said 73% of the polling stations are open and working.
He said: "The members of the polling stations have a telephone to contact technical assistance. Contact them, be patient and for each problem, there is a solution."
"We demand the immediate resignation of Enric Millo for his responsibility in the repression of the State.
"We ask people, even thought they are seeing images that seemed only possible in the era of black and white TV, to continue with the commitment and go to vote."
Asked if the trouble was “worth it” Mr Turull said: "Defending democracy will always be worth it, surrendering to the state is not worth it."
Catalonia's regional government said it would allow voters in Sunday's banned independence referendum to vote at any polling station they found open in the region, if their designated voting booth was closed.
In a further step to make it easier to vote, voting slips printed at home will be accepted as valid, Jordi Turull, the regional government's spokesman told a news conference.
After a court banned the vote, Spanish police arrested Catalan officials, seized campaign leaflets and sealed off many of the 2,300 schools designated as polling stations.
Thousands of Catalans gathered at designated polling stations on Sunday morning as they sought to defy Spanish authorities by voting in the banned independence referendum that has raised fears of unrest in the wealthy northeastern region.
At some stations, voters blocked doors in anticipation that police could try to enter and take over the sites. At one, a Barcelona school, organisers asked people to use passive resistance if police intervened.
"I have got up early because my country needs me," said Eulalia Espinal, a 65-year-old pensioner who started queuing with around 100 others outside one polling station, a Barcelona school, in rain at about 5am.
"We don't know what's going to happen but we have to be here.”
Organisers had asked voters to turn out hours before polling stations were supposed to open at 9 am, and called for "massive" crowds by 7.30am, hoping for this to be the world's first image of voting day.
Leading up to the referendum, Spanish police arrested Catalan officials, seized campaigning leaflets, sealed off many of the 2,300 schools designated as polling stations and occupied the Catalan government's communications hub.
But Catalan leaders, backed by pro-independence supporters, have refused to abandon their plans. Families have occupied scores of schools earmarked as voting centres, sleeping overnight in an attempt to prevent police from sealing them off.
If some voting goes ahead, a "yes" result is likely, given that many unionists are not expected to turn out.
Voters in the region said it was the "most important" say of their lives after living under a "dictatorship".
