Dynamo Dresden face a ban from next season's DFP Pokal after their fans rioted before the away tie at Hannover on Wednesday.
The Bundesliga II club were fined €100,000 after violence during a cup tie against Dortmund last season, and the German FA (DFB) will consider its options - including an expulsion - after a tribunal has investigated what happened.
"What happened has to be analysed and all reports have to be taken into consideration," the DFB general secretary, Helmut Sandrock, said. "This is what the sports tribunal will do. In the past, it has acted with sound judgment."
Dresden issued an apology for the incidents, which happened before the match - lost by Dresden on penalties.
As police marched 1,400 travelling fans to the stadium, bottles were thrown at officers and flares were lit.
On arriving at the stadium, some 300 Dresden supporters were involved in scuffles with officers after climbing fences to get into the ground. Three policemen and a security officer were injured.
"This was an extremely frightening and violent scenario," Hannover police spokesman Dirk Hallmann said. "We don't understand why Dresden fans have to behave like this."
On Thursday, the club released a press statement condemning the violence and saying: "It embarrasses and outrages us that those events happened around the game.
"We are a sports club with a limited influence, but will take responsibility and take the next logical steps possible for us."
During last year's second round match in Dortmund, Dresden fans brought the match to a halt twice, and close to abandonment, by throwing fireworks on to the pitch.
The DFB said at the time that the €100,000 fine it imposed was "a last warning" for the club.