Sixty people are currently receiving medical treatment, Stephan Scharf said.
The regional train was on its way to Munich when it derailed near Burgrain, north of Garmisch-Partenkirchen, a ski resort in the Bavarian Alps.
The accident happened on the last day of school before Pentecost, a religious holiday in Bavaria. It was not immediately known how many students were on board when the train derailed.
Photos and videos of the scene shared on social media show that the wagons of a two-story regional train rolled down an embankment and were trapped in leafy trees, while rescue workers were carrying people with bunk beds.
A major emergency services operation is still underway, Scharf said. Upper Bavaria police have taken over the rescue operation.
This is a groundbreaking story.