More than 600 police and rescue workers -- from Germany and neighboring Austria -- scrambled to the crash scene, which is in a hilly, forested region. Dobrindt said police were on the scene within minutes of the crash.
Helicopters and boats ferried the injured to hospitals and clinics. Authorities said it took about three hours to remove the victims from the scene.
German official: We can't yet determine cause of crash
German official: We can't yet determine cause of crash 01:55
Medical authorities have issued an urgent call for blood donations to help treat the injured, and counselors are being deployed to assist victims and their families. Dobrindt said that emergency workers would also need counseling for what they had faced.
A journalist at the scene, Stephan Richter of German broadcaster RTL, told CNN that the Mangfall Valley Railway was one of the most important lines in the region, used by workers commuting from Bavarian villages to Munich.
It was a small mercy that the train was not as full as it usually would be, because of a school holiday for the annual Carnival celebration, he said.
"We can only pray right now that the train was not packed out like on a regular basis," he said.
German Chancellor Angela Merkel said in a statement Tuesday that she was shocked and saddened by the disaster. "My sympathies go out especially to the families of the nine people who lost their lives," she said.