At 21.20 hours on 26 September 1940 the unescorted and neutral Siljan was hit on port side forward by one G7e torpedo from U-46 about 360 miles west of Cape Clear, Ireland. The ship settled by the bow and the crew began to abandon ship when the U-boat went closer to read her name. They suddenly realized that the ship was still making headway at 6-8 knots and turned towards the U-boat, which had a hard time avoiding a collision and went onto a parallel course just beneath the vessel and came clear after a few minutes, but the diving planes were damaged and the U-boat was forced to abort the patrol. The ship sank after 25 minutes without being identified by the Germans.

The survivors were evenly distributed over three lifeboats which later lost contact with each other. The boat in charge of the master made landfall at Ballydavid, Ireland after a strenuous voyage of nine days. The nine occupants of the second officer’s boat were picked up after six days by the French fishing trawler Auguste Maurice and landed in a French port. However, the lifeboat in charge of the chief officer with nine men aboard was never seen again.