Police cleared most of the occupied Gerhart-Hauptmann-Schule on Ohlauer Strasse in the Kreuzberg area of the city in June, sparking protests around the area.
But a handful of refugees and protesters have remained - until now.
Authorities have given them an ultimatum to leave the buildings by midnight on Friday.
But those left in the school, which has been occupied by around 200 refugees since November 2012, look set to ignore the ultimatum.
Mayor for Friedrichshain-Kreuzberg, Monika Herrmann, told Inforadio on Friday morning that talks were still continuing with the refugees.
Authorities have said they want to resolve the stand-off peacefully, but will clear the school by force as a last resort.
Herrmann said on Friday there would not be an immediate clearance of the buildings at midnight if no resolution was found by then.
There have been protests and some minor scuffles between demonstrators and police at the site this week.
One person was killed and several injured during clashes at the school over the last two years.
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