One demonstrator was injured in a confrontation with police in the central Noerrebro district, according to Denmark's TV2 news channel.
The city's ambulance service said one person had been taken to a hospital.
Earlier on Friday morning, a dozen demonstrators occupied the headquarters of the Social Democratic Party to protest against the eviction and demand that Copenhagen's mayor take action to give the squatters a new house.
They left peacefully after a few hours when police ordered them to vacate the building.
Of the 217 arrested on Thursday, more than 50 were detained pending charges against them for obstructing police from carrying out their duties.
Anticipating more violence, Torsten Hesselbjerg, the country's police chief, said Denmark had borrowed 20 vans from neighbouring Sweden.
Hesselbjerg said: "We want to make sure (Danish) police would not end up in a situation where we lack vehicles that can resist cobble stones if the situation in Copenhagen's streets should escalate further."
Several shops in the area where of Thursday's clashes took place had boarded their windows fearing more violence.
Some of those arrested and injured Thursday included foreigners who had joined the protests that started in the morning after a helicopter hoisted anti-terror police onto the building and evicted the 35 squatters inside.
Twenty-one people from Germany, Sweden, Italy, Greece, United States, Lithuania, Norway, Britain and France were among the arrested.
The eviction angered youths who have viewed the building, a former theatre in central Copenhagen, as free public housing for years.
It has also been a popular cultural centre for anarchists, punk rockers and left-wing groups, where performers have included Australian musician Nick Cave and Icelandic singer Bjork.
Lene Espersen, Denmark's justice minister, said protesters "misused their right to demonstrate" when they became violent.
She said: "I vigorously urge the young people and their supporters to regain their composure. Their anger must not unleash violence and vandalism."
The eviction of the building had been planned since last year, when courts ordered the squatters to hand it over to a Christian congregation that bought it six years ago.
The squatters refused, saying the city had no right to sell the four-story building while it was still in use.