The flight took off just after 6 PM, bound from Tokyo International Airport to Osaka International Airport. As the aircraft reached cruising altitude over Sagami Bay, its tailplane buckled, shedding 15 feet of leading edge into the sea, depressurizing the cabin, and disabling the aircraft's hydraulics. The pilots set their transponder to broadcast a distress signal to air traffic control in Tokyo, which ordered the aircraft to descend and gave it heading vectors for an emergency landing.
After descending to 13,500 feet, the pilots reported that the aircraft was "uncontrollable." It flew over the Izu Peninsula, headed for sea, then turned back toward shore and descended to below 7,000 feet before the pilots managed to return to a climb. The aircraft reached an altitude of 13,000 feet before entering a wild descent and disappearing from radar at 6,800 feet.
Because of rain, unfavorable terrain, and the lack of sunlight, rescue crews were unable to reach the site until the following morning. Most of the passengers' remains were unidentifiable, and were enshrined at a nearby village.
The cause of the crash was determined to be a maintenance error seven years previously. At that time, the aircraft's rear bulkhead was damaged following a bad takeoff. Boeing's procedures called for a doubler plate with two rows of rivets to cover up the damaged bulkhead, but the engineers fixing the aircraft used two doubler plates with only one row of rivets. JAL accepted partial responsibility for the disaster because the tail had been making intermittent whistling noises (suggesting a flaw in the fuselage) for years, without action by company maintenance personnel.