Bombardier, for its part, dismissed the complaints as "without merit" and "defamatory".
Deutsche Bahn said in a statement it is claiming €350 million euros in compensation from Bombardier Transportation Deutschland because it has had to replace the wheels and wheelset axles of the trains and also modify or replace braking systems and the traction motors.
"Over the past months, Deutsche Bahn has tried to reach an agreement by way of an amicable settlement, but to no avail," the company complained.
"Following the expiry of the standstill period, we have now opted to clarify our claims in court," it said.
But Bombardier dismissed Deutsche Bahn's action, saying the rail operator was responsible for maintenance of the trains.
"Bombardier Transportation publicly refutes the claims of Deutsche Bahn... as without merit and the allegations as defamatory. Bombardier reserves all its rights with regard to these defamatory accusations," it said in a statement.
General warranty for the trains had ended in 2007 "by mutual agreement," Bombardier said.
"From the start, S-Bahn Berlin has been responsible for its own maintenance. Bombardier Transportation has no contractual obligations regarding the maintenance and repair" of the particular series of trains, it insisted.
But it added: "Bombardier Transportation believes that prolonged litigation is not in the interests of either company and remains open to dialogue with Deutsche Bahn."
Deutsche Bahn is already suing Bombardier for €160 million in compensation for other problems with more than 200 regional trains operation in southern Germany and problems with the brakes in regional and local trains in Munich.
Bombardier, alongside rival Siemens, is the most important supplier of trains to Deutsche Bahn and primarily supplies local and regional trains.