Investigators believe the fire in Nauen, west of Berlin, was started deliberately. No-one was injured.
Far-right protesters have demonstrated against asylum seekers in the area.
German Chancellor Angela Merkel earlier condemned violent protests at an asylum shelter in the eastern town of Heidenau, near Dresden, at the weekend.
Dozens of police officers were injured in the clashes.
Mrs Merkel has described the behaviour of far-right activists in Heidenau as "abhorrent" and "shameful" and said she would be visiting the town on Wednesday.
Germany expects up to 800,000 people to seek asylum by the end of 2015.
Correspondents say most Germans have been welcoming to refugees, but a small minority has been vocal in its opposition.
The blaze gutted the gymnasium - part of a vocational school - in the early hours of Tuesday.
The building, about 15km (9 miles) west of Berlin, was due to house some 130 people applying for asylum in Germany, reports say.
Police said it was "highly unlikely" that the fire was caused by a technical default and instead were treating it as an arson attack.
Far-right activists in Germany are suspected to have burned down a number of other buildings intended to be used as accommodation for asylum seekers in the past year.
Dietmar Woidke, state premier for Brandenburg where Nauen is located, on Tuesday promised a zero tolerance approach to "any form of xenophobia".
Vowing to bring the fire's perpetrators to justice, he said actions against refugees and asylum seekers were "shameful and unworthy of Germany".
Blockade
Security was increased at a newly-opened centre in Heidenau at the weekend after two nights of protests.Police had to use tear gas and pepper spray in the early hours of Saturday morning to lift a blockade of the shelter. Hundreds of people hurled bottles and stones at police, injuring 31 officers.
Left-wing activists staging counter-demonstrations also clashed with the right-wing protesters.
Vice Chancellor Sigmar Gabriel visited Heidenau on Monday and Interior Minister Thomas de Maiziere promised to use "the full force of the law" against anyone who carried out anti-refugee violence.
ed arson attack.
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