City officials say they are willing to negotiate with the refugees about their demands, but only if they leave.
Four arrests were made on Thursday while activists also forced their way into the German Embassy in the Belgian capital, Brussels.
Protesters entered the embassy, and others invaded a local council building in Berlin, to support the refugees.
Activist Emilie Scholten from the expat volunteering group Give Something Back to Berlin told The Local: "When I spoke to some of the inhabitants of the school on Tuesday they were all very scared and did not know what was going on.
"The refugees had organised a solidarity concert in the school yard for 3pm on Tuesday and by around 11pm the police had blocked off all the roads and encroached on to the school.
"In panic, some of the inhabitants spilled petrol all over the school and threatened to set it alight. Others threatened to jump off the roof.
"Some people were allowed to enter the school to gather their belongings, some were not. There was a real lack of consistency and people feared for their belongings, passports and friends.
"Kreuzberg [the area where the school is] looked like a warzone. I've never seen so many police in my life and it concerns me that innocent people who have come to Germany to flee war and impossible situations are being deliberately confused and intimidated."
Authorities, who are rehousing the refugees in the Spandau and Charlottenburg districts, decided to clear the former school site after dozens of violent incidents.
Over the last 18 months, one person has been killed and several injured in clashes there.
Berlin's Senate says it wants to clear the building peacefully and around 190 of the 211 registered refugees in the school have been given accommodation elsewhere.
