"There were apparently many hundreds of people involved," a police spokesperson told Reuters.
A total of 830 refugees and migrants were present at the facility, and around 20 or 30 people caused the disruption, according to Michael Elias, who is in charge of the shelter.
An unspecified number of arrests were made after around 100 police officers arrived at the scene to restore order.
It came just hours after a brawl at a separate refugee shelter in the Berlin suburb of Spandau forced 500 residents to flee the building in “fear and panic.”
People smashed windows, threw sofas and emptied fire extinguishers, police told AFP, adding that several residents were wounded in the violence.
Germany's police union previously called for refugees and migrants to be separated by religion and country of origin to minimize the potential for conflict as the country struggles to handle hundreds of thousands of new arrivals.
The scuffles come after the police union and women's rights groups accused authorities earlier this year of downplaying reports of sexual assault and rape at refugee shelters because they feared a backlash against asylum seekers from German residents. Interior Minister Thomas de Maiziere has called on Germans to avoid blanket suspicion of refugees.
Germany expects to take in one million refugees and migrants this year alone, and is housing asylum seekers in apartments, army barracks, sports halls, and tent cities.