The German Weather Service (DWD) said northwestern and southern regions are at particular risk as an unstable air mass moves across the country. Authorities have warned that some areas could experience wind gusts of up to 100 km/h.
A yellow 'level one' weather warning was issued for most of the country, with some areas, such as in Thuringia and Baden-Württemberg, receiving an orange 'level-two' warning.
"We have an unusually energy-charged atmosphere," DWD weather expert Peter Hartmann told German newspaper Bild. He added that conditions during the afternoon could develop into "hurricane-force gusts and even tornadoes".
Lower Saxony, North Rhine-Westphalia, Saxony-Anhalt, Brandenburg and Mecklenburg-Western Pomerania are expected to be most affected.
Along the Alpine foothills in southeastern Bavaria, forecasters are warning of heavy rain and hail, although wind speeds are expected to be lower than in northern regions.
Meteorologists have also raised concerns about conditions in central mountain ranges. Trees are vulnerable to strong gusts, causing branches to fall.
People have been urged to be cautious if they find themselves in exposed locations, including the Brocken in the Harz Mountains and Kahler Asten in North Rhine-Westphalia.
The warning comes on a public holiday in Germany as several states mark Fronleichnam or Corpus Christi.
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What can we expect in the coming days?
Conditions are expected to improve on Friday, with a mix of sunshine, clouds and isolated showers forecast.
Northern Germany may still see some thunderstorms. Temperatures are forecast to reach between 15C and 21C.
Further rain and possible storms are expected in southwestern Germany over the weekend. Much of the rest of the country should remain dry with highs of around 23C.
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