The front section of the train derailed on impact, with the train driver sustaining serious injuries, officials said on Saturday. Three more crew members and six passengers were also hurt.
The regional train was heading from Koblenz to Frankfurt.
At the time of the accident, the train was passing a section of the tracks between a rocky hillside and the Rhine River, near the small town of Bacharach. Parts of the railway were also underwater due to heavy rainfall in recent days.
The rain caused several minor landslides in the area, leaving debris on the tracks. Both the tracks and the overhead power cables will need to be fixed before traffic can continue, Deutsche Bahn said.
Police stated that the cliff side also needed to be secured. Trains are running again on the right side of the Rhine river, but parts of the left side are still blocked.
On Friday, two major music festivals in Germany had to be interrupted due to inclement weather - the "Southside Festival" in Baden-Württemberg and the "Hurricane Festival" in Lower Saxony. Dozens of people were slightly injured at the "Southside Festival."
Germany has been facing thunderstorms and sudden drops in temperature for weeks, with several people dying in floods and mudslides.
dj/das/jlw (dpa, AFP)