But German media had reported that a signalling worker had manually deactivated an automatic signalling system to let the first train — which was running late — go past.
That action would have also shut off the braking system.
Investigators said about 150 passengers were on the trains, which would have usually carried more people had it not been winter school holidays in the region.
The accident is 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.