Philippe Cosandey, police spokesman, said shortly after the fire was extiguished that investigators were working on the assumption that its cause was due to "criminal" intent.
However, police later said that the presence of a fusebox in the entrance, where most of the fire damage occurred, suggested the cause of the blaze as accidental.
Nessim Gaon, the owner of the synagogue said: "Either it's an act of God, or it's a terrorist act."
Police said there was no sign of hate messages in the vicinity of the synagogue. However, there have been previous incidents of anti-Semitism in Switzerland.
Anti-Semitic graffiti was found on a Geneva synagogue last year. Switzerland's Jewish community is about 18,000 strong, with about 5,000 Jews living in Geneva.
In March 2005, a fire gutted the library of a synagogue in the southern city of Lugano.
A 57-year-old Italian man was later charged with the attacking the synagogue. Police said he had psychological problems and did not appear to have acted out of anti-Semitism.
Jews say there has been an increase in anti-Semitism in Switzerland following a dispute in the 1990s about the restitution of Jewish funds hoarded by Swiss banks during the Holocaust.