Cantonal police said fire fighters quickly extinguished the blaze at the Albanian Islamic Cultural Association building In Flums after it was reported by a man on his way to prayers at the centre around 6.30am.
Forensic evidence indicated the fire was probably set deliberately, police said, without going into details.
No estimated of damage was disclosed.
But Flums Mayor Christoph Gull told Blick newspaper that surveillance video showed that two molotov cocktails were thrown into the centre, where they exploded in the cafeteria.
Luckily, no-one was in the restaurant at the time otherwise it “would have been fatal,” Gull said.
The mayor said he was “completely surprised” by the act, which he said was not foreseeable.
Arben Sulejmani, president of the cultural association, is mystified by the attack on the centre.
“Last night we were in the restaurant until midnight, laughing and watching football, and then something happened,” Sulejmani told Blick.
“Who did that? Why?”
Saint Gallen police had no immediate explanation.
The cantonal force has put out a public appeal for people with possible knowledge of what happened to step forward.
Anyone with information is asked to call 058 229 49 49.