The two regional trains crashed before 7 am on the single line that runs near Bad Aibling, in Bavaria, and that several wagons overturned, police spokesman Stefan Sonntag told The Associated Press.
Fifty of those hurt have serious injuries, he added.
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"Once that is done then the investigators can begin their work," federal police spokesman Rainer Scharf told the AP from the scene.
The rail line is commonly used by commuters heading to work in Munich, and would normally also carry children traveling to school, but they are currently on holiday, the dpa news agency reported.
It was not clear how fast the trains were travelling at the time of the crash but German rail operator Deutsche Bahn told dpa they were permitted to travel of speeds up to 120 kilometres per hour on that stretch of track.
The trains crashed in a remote area about 60 kilometres southeast of Munich in an area with a forest on one side and a river on the other. Rescue crews using helicopters and small boats shuttled injured passengers to the other side of the Mangfall river to waiting ambulances. Authorities said they were being taken to hospitals across southern Bavaria.
Hundreds of emergency personnel from Germany and neighboring Austria were on the scene looking through the wreckage and aiding in the evacuation of the injured.
"This is the biggest accident we have had in years in this region and we have many emergency doctors, ambulances and helicopters on the scene," Sonntag said.
The two trains from the so-called Meridian line were both partially derailed and wedged against one another, train operater Bayerische Oberlandbahn said in a statement on its website.
It was not yet clear what caused the crash, police said.
Federal Transport Minister Alexander Dobrindt, speaking from the crash scene, said his thoughts were with the family members of the dead and the injured.
"We need to find out know what happened, if the cause of the crash was based on the technology or human failure," he said.
Bayerische Oberlandbahn said it had started a hotline for family and friends to check on passengers.
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