Rescuers were still searching for one missing person in the mangled wreckage in a wooded area near Bad Aibling, a spa town about 60 kilometres southeast of Munich, although police said there was now little hope of finding the victim alive.
One of the trains had sliced into the other, ripping its side apart. Blue, yellow and silver metal debris was strewn around the crash site next to a river in the southern state of Bavaria.
The two drivers and two conductors were among those killed, local broadcaster Bayerischer Rundfunk reported.
German Chancellor Angela Merkel expressed shock at the accident that happened shortly after 7:00 am (0600 GMT).
"I am dismayed and saddened by the serious train accident this morning at Bad Aibling," Merkel said in a statement. "My sympathy goes out especially to the families of the nine people who have lost their lives."
Transport Minister Alexander Dobrindt said the rail track was fitted with an automatic braking system aimed at preventing such crashes, and that investigators were probing if there had been "a technical problem or human error".
Three black boxes on the trains should help shed light on the accident, he said, adding that two had already been recovered, and the third should be found in the course of the day.
The trains collided at high speed on a single track, and the drivers probably did not see each other until the last minute because the crash happened at a curve, said Dobrindt.
"At the moment we will have to wait (for the result of the investigation). Everything else is speculation, and would be unhelpful and inappropriate," he said.
A passenger named as Patrick B. Told local radio Rosenheim 24 that shortly after leaving the station of Kolbermoor, "the train suddenly braked, there was a loud noise and the light went out".
He said he "heard people shouting for help everywhere" and together with a young man, he opened the carriage door using the emergency system.
Some 700 firefighters, emergency services workers and police officers were deployed in the rescue operation, which was complicated because the forest crash site was difficult to access.
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