Police also detained 84 foreigners, including 27 Swedes, 26 Norwegians, 20 Germans, five Dutchmen, two Finns, two Irishmen, one Russian and one American after the clashes.
Munch said: "They will be released tomorrow [Monday] or Tuesday."
The violence followed a peaceful demonstration on Thursday, in an attempt to urge the Copenhagen city council to intervene and stop the eviction of the house's occupants.
City authorities gave a group of young squatters the right to use the four-storey building in 1982, but sold it in 2001 to the Father House community, a small Christian congregation that has tried to evict the youths.
The squatters have refused to leave, saying the city had no right to sell the building while it was still in use.
Denmark's Eastern High Court turned town their appeal on August 28 and ordered them out.