Gale-force winds, torrential rains and hail damaged rail tracks and power lines, forcing trains to be halted between Berlin, Hamburg, Bremen, Kiel and Hanover, the national railway company Deutsche Bahn (DB) said.
A 50-year-old man was killed after his parked car was hit by a tree near the city of Uelzen, also injuring his wife. A falling tree also seriously injured a female cyclist nearby.
Regional train provider Metronom also announced that its services in the northwest of the country were facing serious disruptions after storms had blown trees onto the tracks in several places. Affected services are on the lines between Uelzen, Cuxhaven and Bremen.
Meanwhile flights out of Berlin's two airports were restricted on Thursday afternoon, after the capital was hit by the rough weather.
Road traffic has also been hit by the fierce storms. Transport authorities in Lower Saxony warned on Thursday that drivers on the Autobahn between Hamburg and Hanover should drive with care due to trees lying on the asphalt. Delays are to be expected.
At around 11.30am on Thursday, a tornado was spotted around 10 kilometres from Hamburg Airport, according to the German Weather Service (DWD).
But DWD tornado specialist Andreas Friedrich said the twister was relatively weak and only lasted for a few minutes. It also only came into contact with the ground for a short period of time.
In the south of the city, storms damaged house roofs and killed sheep that were hit by toppled trees.
Music fans had to seek shelter in their cars at the venue of a weekend musical festival near Bremen that, ironically, is named "Hurricane"
Weather service Kachelmannwetter displayed a map of the storm hitting land on Thursday morning.
The DWD warned that further tornadoes are to be reckoned with across the north and east of the country throughout the day.
“The very explosive ingredients” necessary for twisters to develop - a rarity in Germany - all currently exist, Friedrich warned.
The tornado expert said that people who spot a tornado should not view it from their window.
“The best thing to do is to go into the cellar and not to stand near the door or a window,” he emphasized.
The DWD also warned that hurricane-force winds will blast across the north of the country, accompanied by heavy rain.