The German Rail Accident Investigation Agency (Eisenbahn-Unfalluntersuchungsstelle des Bundes, EUB) opened investigation number 04/2016 into the accident.
The German police opened a separate investigation.
Police confirmed that nine of the eleven deaths had been identified as being local men from the districts of Rosenheim and Traunstein aged 24–59.
The cause of this accident was unclear.
By the evening of 9 February 2016, Federal Transport Minister Alexander Dobrindt reported that two of the trains' three train event recorders had been recovered.
The third was still located in one of the wedged train carriages.
On 12 February it was announced that the third event recorder had been recovered.
Police said that the recorder was damaged, but attempts would be made to extract the data.
Data from the other two recorders had thus far provided no indication of human error on the part of the train crew.

In a press conference on 16 February 2016, the local prosecutor (Staatsanwalt) identified "human error" as the cause of the crash.
A train dispatcher at the signalling centre in Bad Aibling had given a wrong instruction.
German investigators said they found no evidence of mechanical failure or technical defects that would have caused the crash.
The dispatcher was also charged with gefährlicher Eingriff in den Bahnverkehr (dangerous interference with railroads), which is punishable with up to ten years' imprisonment.

Many German railway main signals are equipped with an additional subsidiary signal called "Zs 1" (shown as three white dots in a triangle shape).
This subsidiary signal replaces a written order authorising a train driver to pass the signal while it is showing a stop aspect.
The train dispatcher can activate it from the signal box.
There are no safety controls in the signal box, other than special operating rules, for the dispatcher to activate a Zs 1 signal.
When a Zs 1 subsidiary signal is shown to the train driver, he must press and hold the PZB button "Befehl" ("Order") in the cab while moving the train over an active 2000-Hz emergency stop inductor located at the main signal.
A warning tone sounds in the cab to acknowledge to the driver that he is pressing the Written Order button.
If in a station the Zs 1 signal is the last signal, after the complete train has passed the stop signal and any following points(at a speed not exceeding 40 km/h (25 mph)), the driver may continue with normal speed.
The Zs 1 subsidiary signal is supposed to be used only in circumstances when a route for a train cannot be set.
There are sections in the rulebook on how and when it may be activated safely, but according to the local prosecutor, these rules were not adhered to.

In April 2016 it was revealed that the dispatcher had been playing a game on his mobile phone at the time.
After realising he had made an error, allowing both trains to proceed, he dialled an incorrect number when trying to issue an emergency call.
No technical fault existed with either the trains or the signalling system.
With these new findings the prosecutors reversed their initial assumption of Augenblicksversagen (lapse of attention) turning it into a charge of Pflichtverletzung (breach of obligations), which carries a heavier penalty – as a result an arrest warrant was issued, and the train dispatcher was held in pre-trial detention from 12 April 2016.
The prosecutors brought the charges to the court in Traunstein in mid July 2016 with accusations on twelve accounts of fahrlässige Tötung (involuntary manslaughter, i.e. murder by negligence) and 89 accounts of fahrlässige Körperverletzung (involuntary battery, i.e. injury by negligence).
The main trial was scheduled for seven days between 10 November and 5 December 2016.
On the first day of trial the defendant confessed to the charges brought by the prosecutors, but his lawyer wanted the degree of guilt to be evaluated during the subsequent proceedings - although he showed a degree of compassion for the victims, the defendant refused to answer questions on the intensity of his preoccupation with the mobile game.
The German Rail Accident Investigation Agency (Eisenbahn-Unfalluntersuchungsstelle des Bundes, EUB) opened investigation number 04/2016 into the accident. The German police opened a separate investigation. Police confirmed that nine of the eleven deaths had been identified as being local men from the districts of Rosenheim and Traunstein aged 24–59. The cause of this accident was unclear. By the evening of 9 February 2016, Federal Transport Minister Alexander Dobrindt reported that two of the trains' three train event recorders had been recovered. The third was still located in one of the wedged train carriages. On 12 February it was announced that the third event recorder had been recovered. Police said that the recorder was damaged, but attempts would be made to extract the data. Data from the other two recorders had thus far provided no indication of human error on the part of the train crew.
In a press conference on 16 February 2016, the local prosecutor (Staatsanwalt) identified "human error" as the cause of the crash. A train dispatcher at the signalling centre in Bad Aibling had given a wrong instruction. German investigators said they found no evidence of mechanical failure or technical defects that would have caused the crash. The dispatcher was also charged with gefährlicher Eingriff in den Bahnverkehr (dangerous interference with railroads), which is punishable with up to ten years' imprisonment.
Many German railway main signals are equipped with an additional subsidiary signal called "Zs 1" (shown as three white dots in a triangle shape). This subsidiary signal replaces a written order authorising a train driver to pass the signal while it is showing a stop aspect. The train dispatcher can activate it from the signal box. There are no safety controls in the signal box, other than special operating rules, for the dispatcher to activate a Zs 1 signal. When a Zs 1 subsidiary signal is shown to the train driver, he must press and hold the PZB button "Befehl" ("Order") in the cab while moving the train over an active 2000-Hz emergency stop inductor located at the main signal. A warning tone sounds in the cab to acknowledge to the driver that he is pressing the Written Order button. If in a station the Zs 1 signal is the last signal, after the complete train has passed the stop signal and any following points(at a speed not exceeding 40 km/h (25 mph)), the driver may continue with normal speed. The Zs 1 subsidiary signal is supposed to be used only in circumstances when a route for a train cannot be set. There are sections in the rulebook on how and when it may be activated safely, but according to the local prosecutor, these rules were not adhered to.
In April 2016 it was revealed that the dispatcher had been playing a game on his mobile phone at the time. After realising he had made an error, allowing both trains to proceed, he dialled an incorrect number when trying to issue an emergency call. No technical fault existed with either the trains or the signalling system. With these new findings the prosecutors reversed their initial assumption of Augenblicksversagen (lapse of attention) turning it into a charge of Pflichtverletzung (breach of obligations), which carries a heavier penalty – as a result an arrest warrant was issued, and the train dispatcher was held in pre-trial detention from 12 April 2016. The prosecutors brought the charges to the court in Traunstein in mid July 2016 with accusations on twelve accounts of fahrlässige Tötung (involuntary manslaughter, i.e. murder by negligence) and 89 accounts of fahrlässige Körperverletzung (involuntary battery, i.e. injury by negligence). The main trial was scheduled for seven days between 10 November and 5 December 2016. On the first day of trial the defendant confessed to the charges brought by the prosecutors, but his lawyer wanted the degree of guilt to be evaluated during the subsequent proceedings - although he showed a degree of compassion for the victims, the defendant refused to answer questions on the intensity of his preoccupation with the mobile game.
Bad Aibling rail accident