Police descended on the An'Nur mosque on Wednesday morning to conduct a search of the building and three other houses in the area after receiving evidence against four people, Zurich's public prosecutor's office said in a statement.
The investigation relates to a sermon given by the mosque's Ethiopian imam on October 21st in which he “called for the murder of Muslims who refuse to participate in communal prayer”, said the statement.
He also called for those present at the sermon to denounce such people.
The imam and three others are now facing criminal proceedings.
The role of the three other people in relation to the sermon is still unclear and the subject of ongoing investigation, said the prosecutor's office.
A further four men aged 23 to 25 were arrested during the raid for immigration-related offences, said Zurich cantonal police.
It's not the first time the controversial An'Nur mosque has hit the headlines.
In June prosecutors arrested a man thought to be a key figure behind the radicalization of young Muslims in the Winterthur area.
A convert to Islam, he had close ties to the inner circle at the An'Nur mosque, the media said at the time.
Winterthur is considered a hotspot for Islamic radicalization in Switzerland with at least five young men having left the city to travel to Iraq and Syria to fight for Islamic State.
According to Tages Anzeiger, the mosque's previous imam was forced to step down after accusations of extremist views.
The mosque has denied any connection to the radicalization of young people.