Speaking to Blick, police spokesman Andreas Knuchel confirmed that an operation was underway at the King Faysal mosque, initiated by the federal migration office.
One reader told the paper that roads were closed by police and no one was allowed to enter or leave the mosque.
Two people believed to be living illegally in Switzerland were arrested during the operation, said news agencies.
It was carried out peacefully and without incident, said police.
The King Faysal mosque has hit the headlines several times in recent years over suspected links to radical Islam.
The father of the two Muslim boys who refused to shake their female teachers' hands at school is an imam at the mosque.