Zurich District Prosecutor Michael Scherrer told The Associated Press on Tuesday that the artist was under investigation for incitement to violence and for allegedly breaching Swiss law protecting religion during a concert in the city in February 2001.
The religious group, the Swiss-based Christians For Truth, did not mention any particular aspect of the concert when it lodged its formal complaint about the singer.
Manson — whose real name is Brian Warner — and his band members take their first names from pop culture icons and their surnames from famous serial killers. Manson also uses the sobriquet "Antichrist Superstar" and is known for his macabre lyrics.
Baptized as a Satanist and an honorary priest in the Church of Satan, Manson has ripped a Bible during previous stage shows.
His act has made him the target of religious and conservative groups around the world.
Scherrer said he interviewed Manson ahead of another sellout concert Sunday at a Zurich stadium, part of the artist's ongoing European tour. Christian groups and lawmakers in Zurich had tried unsuccessfully to have the latest concert banned on grounds that Manson's views were offensive to a majority of the population.
The rocker rejected the accusations, Scherrer said. Manson cited artistic freedom and said his act was meant to provoke a debate about violence and religion, the official added.
Scherrer said he had yet to decide whether to charge Manson.