It was unclear how many people were inside the house when police began the eviction, shortly after 7am (0600 GMT), by hoisting down members of Denmark's anti-terror police from a helicopter on to the building's roof.
Protesters gathered behind police lines shouting "stop police brutality", while a number of shop-owners boarded the windows of their premises in anticipation of violence.
Activists also erected barricades with garbage containers in several places in downtown Copenhagen and threw stones at the police.
Larsen said police officers from across the country were on their way to Copenhagen to help in the coming days.
Squatters have been using the building since 1982, but in 1999 Copenhagen city council sold the property to a group called Human A/S which then sold it to the Faderhuset Christian group.
The eviction has been planned since last year, after two courts ordered the squatters to leave the house and hand it over to the Christian organisation.
But the squatters refused to leave, saying the city had no right to sell the four-story building while it was still in use.
They have demanded another building as a replacement, and a foundation backing the squatters has offered to pay 12m kroner ($2.1m) for another facility.
Danish police were also reported to be monitoring border crossings with Sweden and Germany after squatters used a website to called for foreign activists to come and help.
In the southwestern Swedish city of Malmo, three men were arrested, suspected of heading to Copenhagen to join the protests, Merima Lulic, a spokeswoman for the Swedish police, said.
She said the men were in possession of explosive materials, but that it was not immediately clear what kind of explosive material they were carrying.
"You could tell they were on their way to start riots," Lulic said.
Police in Stockholm, Sweden's capital, said they were also bracing for a counter demonstration in a downtown park.