Hundreds of rescuers were scouring for more passengers trapped in the wreckage in a wooded area near Bad Aibling, about 60 km southeast of Munich.
At least two carriages from one train were overturned, while the front of the other was crushed. Metal debris was strewn around the crash site.
Hundreds of thousands of people packed the streets of Köln for its annual Rose Monday parade, the culmination of five days of carnival festivities that took place amid heightened security following robberies and sexual assaults in the city on New Year’s Eve.
Police doubled the number of officers they had on hand this year in an effort to reassure the public in the wake of the December 31 attacks primarily targeting women and blamed largely on foreigners.
Throughout Monday morning, police said they had recorded 542 criminal complaints, including 45 allegations of sexual offences, including rape. The numbers were roughly in line with 2015, when police said there were 50 sexual offences reported through the full five-day carnival.
The fire which broke out on Monday afternoon quickly spread across the plant, but officers were able to evacuate the 200 to 250 workers at the factory, and saved 1,000 pigs.
Two people were injured in the fire, which was finally extinguished early on Tuesday.
Clouds of smoke from the blaze drifted across the city and residents were advised to keep windows and doors closed.
The cause of the fire is unconfirmed, but is thought to have started at a defective conveyor belt in the storage hall.