"We condemn the horrific scenes that took place before Thursday's game in Nice in the strongest possible manner," club president Werner Wolf said in a statement on the football team's Twitter account.
An hour before the scheduled kick-off of Thursday's opening match at the Allianz Stadium, several hundred hooded fans in the Cologne colours invaded the Nice stands.
Clashes erupted, with some fans armed with chairs or iron bars torn from the stadium, and a total of 32 people were injured, including two police officers and a steward.
Four were hospitalised, with one -- a Parisian who had been among the German supporters -- in a critical condition after falling in the mayhem.
The club would "do everything in our power to clear up what happened and go with full consequence against those who chose violence," Wolf said.