Investigators say Tuesday's fire in Nauen, west of Berlin, was started deliberately.
No-one was injured in the incident and Police are still searching for the culprits.
Far-right protesters have been demonstrating against asylum seekers in the area in recent days.
The attack comes just days after violent protests took place near another asylum shelter in the town of Heidenau near Dresden over the weekend.
German Chancellor Angela Merkel says the behavior of far-right activists was "abhorrent" and "shameful"
"I want to repeat it again that I condemn in the strongest possible terms the violent outbursts. There was an aggressive mood against foreigners there
