The 58-year-old German national, identified only by the initials T.S.P., was accused of "espionage activity and violation of professional secrecy rules in 45 cases," they said in a statement.
Working at an immigration office in the western town of Ostwestfalen, he accessed databases to pass on information on suspected extremist and opposition members of the religious group, said federal prosecutors.
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He was detained in the town in North Rhine-Westphalia state on February 17 and has been in custody since.
Federal prosecutor filed their indictment on September 7 at the state security division of the Superior Court in Berlin, but only released their statement almost two weeks later, on Tuesday.
Spying for a foreign power carries up to 10 years' jail under German law.
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