Police cordoned off several streets
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Twelve British men are due in court in the Algarve on Wednesday after being charged following scuffles in the resort of Albufeira.
At least 200 football fans, some of them English, clashed with Portuguese riot police on Monday night.
Those due to appear in court have been charged with public order offences and resisting arrest.
One police officer and 10 other people were treated in hospital for minor injuries, police said.
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Isolated incidents of alcohol-fuelled disorder were always anticipated
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One England fan in Albufeira told BBC Radio Five Live that police had been "hitting people indiscriminately".
A Home Office spokesman said of the trouble: "Isolated incidents of alcohol-fuelled disorder were always anticipated, given the combination of alcohol, hot weather and football."
English fans were not the only supporters involved in violence on Monday night.
Portuguese police said they also had problems with German fans in Porto.
Five people were detained after a crowd of 700-800 gathered in a city square and began throwing tables at their Dutch counterparts.
Banning order
Meanwhile, a man from Staffordshire who was the first Briton to be deported from Portugal during Euro 2004 has received a football banning order on his arrival back in the UK.
And police in Wakefield, West Yorkshire, have charged three men following violent clashes on Sunday night.
Albufeira, a resort packed with bars, is the base for the majority of England fans who have travelled to Portugal for Euro 2004.
Officers had moved into an area known as The Strip at around 0130 BST after fans spilled out of bars into the street.
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They began throwing bottles at the police and we had to send in the horses
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Police spokesman Captain Manuel Jorge said a crowd of English fans had been drinking in the street near the La Bamba bar.
He said: "They began throwing bottles at the police and we had to send in the horses to bring the situation under control."
Supporters had also blocked traffic and thrown chairs at police, he said.
'Mayhem everywhere'
One England fan, Pete, who saw the clashes, told BBC Radio Five Live: "One guy threw a glass over the top of everybody, at the police, and then they rushed in.
"They [the police] started hitting people indiscriminately - I saw a girl get hit around the legs and a girl get hit across the face.
He said "it was one person that threw something, which got a lot of people hurt".
Another fan, Gary, said there was "pure mayhem everywhere".
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I've been running bars here for 25 years and I can't quite believe what happened - the police were too nervous
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He said: "Somebody threw a bottle, then the riot police came in, hitting the girl across the head - they were hitting a lot of people across the legs."
Florival Palma, 47, who runs a number of bars in the area, also saw the disturbances and thought "nervous" police provoked the fans.
He said officers became concerned by one group of fans, who were being particularly loud, and hit one man on the legs with a baton.
"Suddenly the chairs, tables and signs started flying.
"There were 50-60 reinforcement police who arrived rapidly, and they chased the England fans off up the street.
"I've been running bars here for 25 years and I can't quite believe what happened. The police were too nervous, it was ridiculous."
England-wide trouble
The Staffordshire man who left Portugal with a 12-month suspended sentence and a fine after he was convicted of assaulting a Frenchman was arrested as he arrived at Heathrow airport on Monday.
Alan John Walker, 29, a Stoke City fan from Leek, was given a three-year football banning order by magistrates in London.
The order forbids him from visiting Stoke town centre or Stoke City's Britannia Stadium during a match, as well as banning him from any town where Stoke City are playing an away match.
Walker recently completed another three-year ban, for pitch invasion.