In a statement, the prosecutor in Zurich's cantonal government said the imam at the An'Nur de Winterhour mosque, who is an Ethiopian national, had been detained for incitement to violence.
During an October 21 sermon, the imam "called for the assassination of Muslims who refuse to participate in communal prayers in the mosque," the prosecutor's statement said, adding that a criminal probe had been launched.
Three of the imam's followers were also being held and investigated but the prosecutor said it was "unclear" what role they played in the alleged call to violence.
Separately, Zurich police raided the mosque early Monday and arrested three other men -- aged 23 to 35 -- over suspected immigration violations.
Swiss media have reported frequently on the An'Nur mosque, including on suggestions that it has played a part in radicalising young Muslims.
According to the news site 20min.ch, the Ethiopian cleric starting working at the mosque recently, replacing a predecessor who was forced to leave amid accusations that he was preaching extremism.
Swiss media have further reported that the compound's landlords do not intend to extend the mosque's lease, possibly forcing its closure by the end of the year.