Local health authorities said 27 people were admitted to hospital with slight to medium injuries, including at least nine police officers. Many others got first aid on the scene.
One police officer opened fire on the demonstrators. Three people are in hospital with gunshot wounds, one of them seriously injured.
Police said live rounds were used because rubber-coated bullets were not available.
Twelve police officers were hurt in the street battles, which raged for several hours.
Swedish radio warned people to stay away from the city centre due to the violence on a day when more than 600 people were detained during 12 hours of rioting.
At a news conference, Swedish Justice Minister Thomas Bodstrom denied that police had lost control of the situation, but he added that police procedures would have to be reviewed.
Event moved
The severity of the demonstrations prompted police to relocate a planned dinner for EU leaders.
Police decided the dinner, originally to be held at the elegant Tragar'n restaurant in the city's Botanical Gardens, would instead be held in the conference centre, which is guarded by hundreds of police.
Four delegations attending the summit were also asked to change hotels after police said they could no longer guarantee their safety from protesters, a spokesman for the Finnish delegation told AFP.
Anti-globalisation and anti-EU demonstrators have been fighting pitched battles with police for two days.
On Friday shops were looted and buildings damaged some distance away from the meeting, where EU leaders discussed ways of putting expansion plans back on track after Irish voters rejected them.
Violence
The protesters, many wearing face masks, threw fireworks and stones at police, who fought back with clubs.
Others were seen shattering shop windows, including a McDonald's restaurant and a bank, and burning cafe furniture along streets littered with debris.
Some mounted policemen were thrown off their horses.
Local health authorities said 27 people were admitted to hospital with slight to medium injuries, including at least nine police officers. Many others got first aid on the scene.
Police sealed off a shopping mall in the centre of town after an object suspected to be a bomb was found.
Demonstrators tried repeatedly to get close to the conference hall where the 15 EU leaders are meeting, and at one stage were reported to be less than a mile away.
Swedish Prime Minister Goran Persson, whose country holds the rotating EU presidency, said he was upset by what he called "this destructive behaviour".
"This is a blatant disregard for democracy and unworthy of a society such as ours," he added.
At least 440 people were arrested on Thursday after clashes during US President George W Bush's meeting with EU leaders and police said more were detained in the second day of riots.
Irish "no"
The Irish rejection of the Nice Treaty has shattered Sweden's hopes that it might be able to end its EU presidency next month by announcing an entry date for new members.
Irish Prime Minister Bertie Ahern asked EU leaders to grant his country "an extended period of reflection" after last week's "no" vote.
"I want to make it absolutely clear that, in my view, the 'no' vote should not be interpreted as a vote against enlargement," Mr Ahern told his EU colleagues at the start of the summit.
Ireland is the only country that requires a referendum to approve the EU treaty, and EU leaders hope that the expansion plan will be ratified in a second vote once Irish concerns about neutrality are allayed.
The EU entered membership negotiations with six countries in 1998 - the so-called wave one, which includes Poland, Czech Republic, Slovenia, Hungary, Estonia and Cyprus.
Although no date has been set for their entry, these countries could join the European bloc by 2004.