The head-on crash happened at Bad Aibling, a spa town about 60km (37 miles) south-east of Munich.
One of the trains was derailed in the crash and several carriages were overturned, German media reported.
Roads around the scene have been closed and the railway line between Holzkirchen and Rosenheim is blocked, local media reported.
He said the two regional trains had collided on a single track between Rosenheim and Holzkirchen shortly before 07:00 local time (06:00 GMT).
Although the train was carrying commuters, local carnival holidays meant no schoolchildren were on board, according to reports.