They Washington Post reports that two trains were involved in the crash near Bad Aibling, in Bavaria.
It was not immediately clear how many people were injured, but a spokeswoman for police in Upper Bavaria confirmed to German news agency DPA that there were deaths.
DPA reported that one train derailed in the crash Tuesday morning, and several wagons overturned.
It said eight rescue helicopters were standing on a lawn near the entrance to the town of Bad Aibling and further rescue staff were on the way to the scene of the crash.
Police spokesman Stefan Sonntag has confirmed that trains on a single track between Rosenheim and Holzkirchen collided just before 7am local time.
Mr Sonntag said the scene of the accident is so chaotic, there are no specific numbers over the amount of dead or injured.
However, police at the scene have confirmed that the number of people “very seriously” injured has risen to 15, while the death toll has risen from an initial report of 4 to 9people killed.
Mirror UK reports that the trains were operating on a single track.
Rosenheim police spokesman Rainer Scharf confirmed the report to German radio station N24.
Passengers are understood to still be trapped in the train – some having to be cut out.
With the train being on a single track, that may indicate a signalling failure but that is not confirmed by authorities.
German media reports are now indicating that there are 150 people injured, initial reports said that 100 had been injured in the incident.
Authorities say it remains unknown what the cause of the crash is, meanwhile, nearby roads have been closed as emergency services race to the scene.
Bernd Rosenbach, managing director of Bayerische Oberlandbahn which operates Meridian trains, told reporters: “The accident is a huge shock for us. We are doing everything we can to help the travellers, relatives and workers.”
Technical manager Fabian Amini added: “Our thanks go to the emergency services and workers who gave their help so quickly.”
BBC reports that although the trains were carrying commuters, local carnival holidays meant no schoolchildren were on board.
The scene of the crash is close to the Mangfall river in a hilly and densely wooded region. Casualties were being evacuated by boat and by helicopter.
Several hundred emergency services personnel were at the scene and rescue teams from nearby Austria were also helping, local media said.
By midday, police said all casualties had been removed from the wreckage, however, some reports suggests that two people are still missing.
The German transport minister, Alexander Dobrint, commended the rescue operations, he also noted that it would be too early to speculate as to the cause of the crash.
Dobrint said the two passenger trains that crashed in Bavaria were on a curve and it appears that neither had time to brake before they hit head-on.
While noting that the stretch was fitted with a safety system designed to automatically stop trains to prevent such a crash, he said “it’s not clear why it didn’t function, we have to assume that the train drivers had no visual contact and hit each other without braking.”
He however, added that there are three brain-boxes that needs to be recovered to be certain of what went wrong.
The minister informed that two of the brain-boxes in question had been recovered, while the search for the third remains ongoing.
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