Four residents of the hostel are to appear in court charged in connection with a disturbance. A fire at the facility caused some damage and eleven people were injured.
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Emergency services were called to the migrant center in the northern Bavarian town of Bamberg on Tuesday after a disturbance.
Men reportedly threw stones and other objects at police before barricading themselves in a building.
A fire then broke out.
Police said nine people had to be treated for smoke inhalation and two others were also injured.
Quadriga - Refugees in Germany - Angst on both Sides
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Police characterized the events as a disturbance of the peace and opened an investigation. Four main suspects are due to be brought before the investigating judge on Wednesday.
Bavaria shares its southern border with Austria. In August it set up seven migrant centers with the aim of speeding up asylum claims.
The facility in Bamberg offers space for up to 3,400 people.
Police said about 1,250 asylum seekers were currently there.
Bavaria opens 'Anker' migrant transit center
The southern German state of Bavaria has opened the first controversial center to process migrants arriving through the Austrian border. The facilities are part of a plan to reduce the number of asylum seekers.
Image: picture-alliance/dpa/S. Puchner
First migrant center opens in Bavaria
The centers are part of the "migration master plan" of Interior Minister Horst Seehofer. The concept behind the centers is that asylum seekers will be kept there until their right to stay is determined.
Image: picture-alliance/dpa/S. Puchner
Controlled immigration
Bavaria will set up a total of seven "Anker" centers, each holding between 1,000 and 1,500 refugees. The name derives from the German words Ankunft, Entscheidung, Rückführung (arrival, decision, return). The aim is to create a sort "one-stop" center with all the relevant government agencies required to complete the entire asylum process represented on site.
Image: picture-alliance/dpa/S. Puchner
Critics warn of ghettoization
Church groups, refugee advocates and opposition parties have all voiced their concern, describing the centers as deportation camps and warning of the ghettoization of migrant communities. The NGO Save the Children said the centers were "no place for children," as they facilitated "tension and aggression."
Image: picture-alliance/dpa/S. Puchner
Compromise solution
The centers are the result of a last-minute political deal between Chancellor Angela Merkel and Interior Minister Horst Seehofer. His initial plan to turn migrants away at the border created a political crisis that could have toppled the coalition government of Merkel's Christian Democrats, their Bavarian sister party the CSU and the Social Democrats.
Image: picture-alliance/dpa/K. Nietfeld
Little enthusiasm for centers in Germany
The decision to create the centers was taken at federal government level, but responsibility lies with Germany's individual states. Bavaria — where Seehofer's conservative CSU faces a crucial state election in October — has taken the initiative. But others have delayed the establishment of the migrant transfer centers or refused to take part in the policy.