Investigators will have to find out why a train that left Holzkirchen travelling east to Rosenheim was on the single track at 06:48, four minutes after it was due to reach its next stop at Kolbermoor, where it would have met the westbound train on a double track.
The westbound train from Rosenheim to Holzkirchen would have left Kolbermoor at 06:45 and would have been expected to be on the single track at the time of the accident.
The controller's role was initially highlighted by newspaper group RedaktionsNetzwerk Deutschland (RND), which quoted sources suggesting the safety system had been switched off to allow the eastbound train through on the single track line because it was several minutes late.
That would also have made the automatic braking system inactive. That braking system, known as PZB, is supposed to kick in when a train runs through a red light and was installed after a 2011 disaster at Magdeburg in which 10 people died.
Sueddeutsche Zeitung, citing a well-informed source, alleged that when the signal controller had realised his mistake it was too late.
A police spokesman rejected the theory as "pure speculation".