Typhoon No. 15, Marie, which had blown through Honshū, was in the Sea of Japan at 12:00 on September 26, 1954, heading northeast and had wind speeds of more than 100 kilometers an hour. It was predicted to reach the Tsugaru Strait at around 17:00.
At 11:00, the Tōya Maru arrived at Hakodate after its first journey that day from Aomori. It was originally scheduled to return at 14:40, to arrive at Aomori just before Typhoon Marie. However, due to the expected storm, another ferry—the Dai 11 Seikan Maru, a somewhat poorer quality vessel—could not depart on its scheduled journey to Hakodate. Therefore, passengers and vehicles were transferred to the Tōya Maru, delaying its departure.
The captain of the Tōya Maru decided to cancel its journey at 15:10.
At 17:00, following heavy rainfall in Hakodate, the weather cleared up and the outlook improved. The captain, presuming that the typhoon had now passed as predicted, decided to proceed with the journey to Aomori. However, by this time the typhoon had only slowed down and was predicted to remain over the strait for an entire day.
Atypically, the typhoon gained strength in the Sea of Japan. It was considered to have already become an extratropical cyclone when it reached Japan.
At 18:39, the Tōya Maru departed from Hakodate with approximately 1,300 passengers aboard. Shortly thereafter, the wind picked up coming from a SSE direction.
At 19:01, the Tōya Maru lowered its anchor near Hakodate Port to wait for the weather to clear up again. However, due to high winds, the anchor did not hold and Toya Maru was cast adrift. Water entered the engine room due to the poor design of the vehicle decks, causing its steam engine to stop and the Tōya Maru to become uncontrollable. The captain decided to beach the sea liner onto Nanae Beach, on the outskirts of Hakodate.
At 22:26, the Tōya Maru beached and an SOS call was made. However, the waves were so strong that the sea liner could no longer remain upright and at around 22:43, the Tōya Maru capsized and sank at sea several hundred meters off the shore of Hakodate.
Of the 1,309 on board, only 150 people survived, while 1,159 (1,041 passengers, 73 crew and 41 others) died.
Among those killed were 35 American soldiers from the U.S. Army's 1st Cavalry Division Artillery who were traveling from Hokkaidō as an advance party to set up a new camp (Camp Younghans) at Higashine, Yamagata, near Sendai. One soldier survived when he was swept through a port hole. Another, 2nd Lt. George A. Vaillancourt, Battery C, 99th Field Artillery Battalion, 1st Cavalry Division, was posthumously awarded the Soldier's Medal, the highest non-combat medal at the time, for his courage during the tragedy. The football field at Camp Younghans was dedicated to Lt. Vaillancourt on September 24, 1955.
Four other ferries sank in the same typhoon, making a total loss of life of 1,430.