The trains were travelling on a single track near Bad Aibling in Bavaria, in the south of the country, when the crash occurred and one of the trains derailed.
An investigation has been launched into what caused the collision, which happened early in the morning.
Rescue teams are on site and helicopters have been transporting some of the injured to nearby hospitals.
Bad Aibling is near the Austrian border and the rescuers are being helped by the Austrian Red Cross. The site, between Rosenheim and Holykirchen, has been sealed off.
The trains’ operator, Meridian, is part of French passenger transport firm Transdev, which is jointly owned by state-owned bank CDC and water and waste firm Veolia. It runs train, tram and bus networks in 19 countries.
State-owned Deutsche Bahn is responsible for the track. The line has a system that makes a train brake automatically if it goes through a red light.