The incident occurred late Thursday on an Intercity Express train, the German equivalent of France's TGV, bound for Frankfurt in western Germany, with around 180 passengers evacuated.
The case has been referred a security service unit in Bonn specialised in handling politically motivated crimes, a police spokeswoman told AFP.
She declined to comment on a report by the German daily Bild that the suspect was believed to be an extreme-right activist with a criminal record.
A police statement said that "a political motive cannot be ruled out at the moment".
Passengers on the train locked the suspect in a bathroom after he set off the pyrotechnics, police said in an earlier statement, adding that the man was carrying two knives.
German media reported the man -- from the western German city of Aachen -- allegedly threatened to carry out an attack and said he wanted to kill people.
Public radio station Deutschlandfunk reported, citing witness statements, that the man threw pyrotechnic devices filled with plastic pellets.
At least 12 passengers were slightly injured, including one who was taken to hospital but was released after treatment, police said.
Police said they searched the train for dangerous objects, but did not find anything.
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