Slightly after 20:00 hours, the master of the "Toya Maru" had his crew members tighten train lashing gears further, check the closure of openings with lids, the free flow of water through scuppers, and put away wooden blocks and wedges. Some closing devices were not in good condition and crew members were not able to completely close them. Meanwhile sea waves simply grew larger and larger, increasing the amount of seawater rushing into the train deck. Because of the sea water which flowed along with the ship's motion, such work became dangerous and workers at last abandoned the operation and left the deck at about 20:30 hours.
The water on the train deck of the "Toya Maru" then reached as high as 0.3 m forward and the aft deck was completely submerged under the sea level, resulting in sea water finding its way into the passage ways on both sides of the same deck through gaps in the watertight doors.
In addition, flooding commenced through the aforementioned openings to the engine room, boiler room, etc. and, despite every measure possible having been taken, one by one generators became incapable of continuing operation making discharge of water impossible. Around 21:50 hours the port main engine fell inoperative, followed by the starboard one at 22:05 hours.
On the bridge of the "Toya Maru", the Master made every effort to hold her anchor position by heading up into the wind through the periodic use of the engines, but as the wind veered to the SW and gained intensity, the vessel commenced to drag her anchors at around 20:00 hours. The sea waves reached a height of 6 m on average and the area around the anchorage was in a confused state of complex waves with the addition of waves reflected by the breakwater. At around 21:00 hours on the same day her list toward the port side increased despite use of the trimming pump, the rate of dragging anchors had accelerated since around the time the port main engine ceased to function, and she came to receive sea waves from the port side, resulting in the hull starting to list toward starboard. The list grew larger as time passed and the Master ordered the Purser at around 22:15 hours to have passengers wear lifejackets.
At around 22:26 hours the "Toya Maru" touched bottom lightly three times in the aft portion at a position, 12.4 m deep and sandy in seabed quality, 267°0.8 miles from Hakodate Port No. 3 Breakwater light beacon, about 0.6 miles off the nearest land, and the vessel listed up to 45°. Thereafter the vessel's bow gradually drifted leeward to starboard and the list increased greater and greater every time she suffered the onset of sea waves, resulting in the trains falling. Finally, at around 22:45 hours the "Toya Maru" listed toward starboard about 135°and sank almost in parallel to the shore line at a position of 337°2,500 m from Hakodate Port Breakwater Light with her bottom floating above the water.
