Federal and local police said the cause of the crash near Riedlingen, roughly 158km west of Munich, remains under investigation.
Photos from the scene showed parts of the train on its side as rescuers climbed atop the carriages.
Roughly 100 people were onboard the train when at least two carriages derailed in a forested area around 6.10pm Sunday (0210 AEST Monday).
The train was on a 90km route between Sigmaringen and Ulm when it derailed.
Storms passed through the area before the crash and investigators were seeking to determine if the rain was a factor.
German Chancellor Friedrich Merz, in a post on social platform X, said he mourned the victims and gave his condolences to their families.
Deutsche Bahn, Germany's main national railway operator, said in a statement that it was co-operating with investigators.
Chief executive Richard Lutz said he will visit the scene of the accident on Monday.
According to Lutz, Deutsche Bahn is deeply shocked and dismayed by the derailment.
"My heartfelt sympathy and condolences go out to the relatives of the deceased. I wish the injured a quick and full recovery," he said.
He said thanks go to all the emergency services and volunteers who are on site.
with DPA
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