Storm Xavier slammed into the country late last afternoon, uprooting trees and flinging signs and billboards to the ground with winds that reached 130 kilometres per hour.
"Most of the train tracks in the north and east of Germany are still unusable," said a spokesman for the rail operator Deutsche Bahn.
Trains linking Hamburg, Hanover and Berlin have been cancelled, as all three cities were severely hit by the storm.
Hundreds of passengers spent the night in the stations, some finding a spot on trains turned into temporary accommodations by Deutsche Bahn.
"The clearing work could last all day," said a spokesman for Berlin's rail service.
The capital's firefighter service said the emergency situation continues, as it called on volunteers to return to help out from 8:00 am (1130 IST).
Seven people died yesterday after their vehicles were hit by falling trees.
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