Berlin police chief Klaus Kandt sent an ultimatum to regional district mayor Monika Herrmann, initially for 7am on Tuesday, requesting that his officers be given permission to clear the Gerhart-Hauptmann-Schule.
On Tuesday afternoon that request came through.
Berlin Police tweeted: "For us that doesn't necessarily mean forced eviction. We will consider our next steps calmly."
But The Local's reporter at the scene said police began clearing protesters away with violence from the cordon outside the school shortly before 4pm.
He reported pepper spray being used and police putting on riot gear to get rid of demonstrators who were sitting down outside a cordon which has been in place around the former school for a week.
"They are wearing helmets and trying to clear protesters," he said. "They're blocking people from going into that area. An announcement was made telling around 200 demonstrators to leave as it was not a legal protest."
A female protester whose nose was bleeding told our reporter: "I'm so angry I can't even go home."
The chants also switched from being about refugees to criticizing the police. “Stupid policemen, murders and fascists,” was one of the chants.
By 4.30pm most of the demonstrators had been cleared.
Protesters read a statement by Hans Pannhoff, a local councillor, at 3.40pm.
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PHOTO GALLERY: Police seal off area of Kreuzberg