State weather service DWD said on Tuesday that 40 litres of rain could fall in an hour in the eastern states of Saxony, Saxony-Anhalt and Thuringen.
Meanwhile, areas of central Germany suffered flooding on Monday night. In Wiesbaden, Hesse, cellars were flooded and the fire service was called out to help with 55 incidents.
Parts of Bavaria also experienced heavy rain and a number of flights were delayed at Frankfurt Airport on Monday after 11pm due to the weather.
The heavy rain is expected to continue in central Germany into Wednesday and Thursday.