Due to heavy fog and other factors, captain Kohei Asoh mistakenly ditched the plane near Coyote Point in the shallow waters of San Francisco Bay, two and a half miles short of the runway.

[5] Actual departure was delayed to 5:36 p.m. (08:36 UTC) due to required maintenance on the pilot's instrument panel, which was providing inconsistent altitude readings.

[1]: 3  Oakland TRACON advised the pilots that local visibility at SFO was 3⁄4 mi (1.2 km) and the runway visual range exceeded 6,000 ft (1,800 m), recommending the flight to hold.

[1]: 3  Commanding pilot Captain Kohei Asoh attempted an automatic-coupled Instrument Landing System (ILS) approach due to the heavy fog,[1]: 5  which he had never done before on a recorded DC-8-62 flight.

[1]: 5  At 9:16 a.m. (17:16 UTC), Bay TRACON instructed Asoh to descend to and maintain 4,000 ft (1,200 m) altitude and turn left to a heading of 040° while holding at an airspeed of 180 kn (330 km/h; 210 mph).

Asoh had set his minimum descent altitude alert to 211 ft (64 m); the alert was triggered by the radio altimeter, as the pressure altimeter was reading 300 ft (91 m) at the time; as Asoh checked for runway lights, copilot Hazen called out visual updates: "[we are] breaking out of the overcast — I cannot see the runway light — we are too low — pull up, pull up".

[7] In fact, the plane came to rest on the Bay floor in shallow water approximately 7 feet (2.1 m) deep,[8] leaving the forward exits above the waterline.

[4] The chief purser, Kazuo Hashimoto, felt there was no panic amongst passengers after landing, and tried to make an announcement with the public address (PA) system.

Since the PA system had failed after the landing, he ended up shouting from the forward cabin for passengers to "Be quiet, the plane has reached the bottom of the sea.

"[9] The passengers and crew all evacuated the plane on lifeboats, which were towed by police and Coast Guard boats to the nearby Coyote Point Yacht Harbor.

This deviation from the prescribed procedures was, in part, due to a lack of familiarization and infrequent operation of the installed flight director and autopilot system."

[1]: 9  After becoming familiarized with the DC-8-62 in April 1968, Asoh piloted approximately one round-trip from Tokyo to San Francisco and back via Honolulu per month, starting in July.

[1]: 9  At the time, Asoh stated (through a translator) that "the plane was fully automatic" and he couldn't "say what was wrong [to cause the water landing]" because he had been in contact with the control tower during the entire approach and was never informed he had deviated from the flight path.

[6] According to the NTSB report, Asoh failed to follow the published Japan Airlines procedures to perform an autopilot-controlled descent from the Woodside Vortac and subsequent automatic-coupled approach on ILS.

According to his statement, Asoh did not set the autopilot for ILS capture until the aircraft had descended to an altitude of 2,500 ft (760 m), when it was already below the required glide slope.