Videos on social media showed streets knee-deep in water and others buried by landslides.
There were no immediate reports of injuries.
Hof county near the eastern border with the Czech Republic issued a disaster alert late on Tuesday as basements filled with water, trees were uprooted and some areas lost power overnight.
Germany’s DWD weather service said the region saw 80 litres (more than 21 gallons) of rain per square metre in the space of 12 hours.
Meteorologists predicted further “extreme storms” in the western and central parts of Germany through Thursday, with peak rainfall possibly reaching 200 litres per square metre.
The neighbouring Netherlands and Belgium were also hit by flooding.
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