Hundreds of rescuers were scouring for more passengers trapped in the wreckage in a wooded area near Bad Aibling, a spa town about 60 kilometres (40 miles) southeast of Munich.
At least two carriages from one train were overturned, while the front of the other was crushed. Blue, yellow and silver metal debris was strewn around the crash site next to a river in the southern state of Bavaria.
READ: At least eight dead in German train crash: police
"We now have nine dead," said police spokesman Juergen Thalmeier. One person was still missing, likely trapped in the wreckage, police added in a statement.
Eighteen people were seriously injured and 90 had light injuries, added police in a statement.
The two train drivers and two conductors were among those killed, local broadcaster Bayerischer Rundfunk reported.
An investigation is ongoing to determine if the accident was caused by "a technical problem or human error," Transport Minister Alexander Dobrindt told rolling news channel NTV from the scene.
Hundreds of 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, said Thalmeier.
Rescuers focused on the impact area of the trains, using electric saws to cut through the mangled wreckage.
Rescue workers from nearby Austria were also on site, NTV said.
Underlining the difficulty of the emergency operation, mountain rescuer Joerg Becker told NTV: "The terrain is not only difficult to access but the large number of injured also requires a massive coordination effort between so many rescue and aid groups."
'Deeply shocked'
"The tragic accident occurred on the single-track route between Rosenheim and Holzkirchen this morning shortly after 7:00 am (0600 GMT)," regional rail company Meridian, a subsidiary of the French group Transdev, said in a statement.
Rainer Scharf, a Bavarian police officer, said that "given the severity of the accident, we believe the two regional trains collided head-on at low speed".
About a dozen helicopters were deployed, with television footage showing them waiting in a clearing outside the forest, from where rescuers were emerging with stretchers carrying the injured.
![Firefighters and emergency doctors work at the site of a train accident near Bad Aibling, southern Germany. - AFP pic](http://img.astroawani.com/2016-02/81455024519_freesize.jpg)
The rail stretch and two nearby roads were closed to traffic.
"The accident is an enormous shock for us," said Bernd Rosenbusch, who heads the Bavarian rail company BOB that operates trains on the route.
"We will do everything to help travellers, their relatives and our employees."
Christian Schreyer, chief executive of Transdev, said: "We are deeply shocked and stunned that something like this could have happened. Our thoughts are with the victims and families of the victims".
After German rail was liberalised at the end of the 1990s, BOB -- a subsidiary of Transdev, became one of the train operators competing with state-run Deutsche Bahn.
Although it has lost its monopoly operating status, Deutsche Bahn still owns the rail network.
The accident is believed to be Germany's first fatal train crash since April 2012, when three people were killed and 13 injured in a collision between two regional trains in the western city of Offenbach.
The country's deadliest post-war accident happened in 1998, when a high-speed ICE train linking Munich and Hamburg derailed, killing 101 people and injuring 88 at the northern town of Eschede.