Three carriages overturned at least partly, and people were pulled out of the windows to safety.
The cause was not immediately clear.
The local government in Garmisch-Partenkirchen said that at least three people were killed, news agency dpa reported.
Sixty people were being treated for injuries, and 16 of them were seriously hurt.
It was not clear how many people were on the train at the time of the accident.
The line between Garmisch-Partenkirchen and Oberau, north of the accident site, was closed.
The area is near the Austrian border.