On 30 September 1957, Unzen, a Japan Airlines Douglas DC-4 caught fire in its number one engine after takeoff from Osaka International Airport, at an altitude of 300 ft (91 m). The aircraft was forced to land in a rice field and was damaged beyond repair.
On 25 April 1961, Hakone, a Japan Airlines Douglas DC-8 from San Francisco to Tokyo, touched down and ran off the end of the 8,900 ft (2,700 m) wet runway at Tokyo International Airport. The aircraft stopped after the main gear entered a ditch 9 ft (2.7 m) wide and 6 ft (1.8 m) deep, located 150 ft (46 m) beyond the end of the runway. The aircraft was shipped back and repaired by Douglas Aircraft Company at Long Beach, CA, United States, and returned to service as a Series 53 with a new registration (JA8008) in early 1963 and was renamed Matsushima.
On 10 April 1962, Haruna, a Japan Airlines Douglas C-54 from Fukuoka to Tokyo, made a wheels-up landing at Osaka. There were no casualties, however, the aircraft was damaged beyond repair and was written off.
On 27 February 1965, Kaede, a Japan Airlines Convair 880 was performing a low pass training near Iki Airport when, at 150 ft (46 m), descended fast and struck the runway. The aircraft slid and caught fire.
On 25 December 1965, Kamakura, Japan Airlines Flight 813 operated by a Douglas DC-8 took off from San Francisco International Airport at 13:08 and suffered an uncontained engine failure on number one engine while climbing through 4,500 ft (1,400 m). A fire erupted in the area of the number one engine, but was quickly extinguished. The aircraft made a safe emergency landing at Oakland International Airport, CA. The probable cause was "a disintegrating engine failure and in-flight fire caused by the failure of maintenance personnel to properly secure the low pressure compressor section torque ring during engine overhaul".
On 26 August 1966, Ginza, a Japan Airlines Convair 880 (leased from Japan Domestic Airlines) yawed left for unknown reasons after the nose lifted up during a training flight at Haneda Airport. Some 1,600 m (5,249 ft) into takeoff, the number one engine struck the runway. The aircraft left the runway and the nose pitched down again. All four engines separated as well as the nose and left landing gear; the aircraft caught fire and burned out. All five crew died.
On 22 November 1968, Shiga, Japan Airlines Flight 2 operated by a Douglas DC-8 accidentally landed in San Francisco Bay approx. 2.5 mi (4.0 km) short of San Francisco International Airport. The aircraft was recovered after being in the water for 55 hours. There were no injuries to the crew or to any passengers. The probable cause was "the improper application of the prescribed procedures to execute an automatic-coupled ILS approach. 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". The aircraft was repaired by United Airlines at San Francisco International Airport and returned to JAL in March 1969. Pilot Kohhei Asoh said that he mistakenly believed that he was landing on the runway when in fact the plane hit the water several hundred yards away.
On 24 June 1969, Kikyo, Japan Airlines Flight 90 operated by a Convair 880 was taking off from runway 32R at Moses Lake Grant County International Airport. The power was reduced on the number four engine during take-off, however, the aircraft continued to yaw to the right until the number four engine struck and slid off the runway. It burst into flames, killing three of the five crew members on board. The probable cause was a "delayed corrective action during a simulated critical-engine-out takeoff maneuver resulting in an excessive sideslip from which full recovery could not be effected".
In 1970, a teenage boy climbed into the cargo area of a Sydney to Tokyo flight. As the plane was taking off he fell to his death. A photographer accidentally captured the whole thing. 
On 14 June 1972, Akan, Japan Airlines Flight 471 operated by a Douglas DC-8 struck the banks of River Yamuna, about 20 km (12 mi) east of New Delhi's Palam International Airport. The crash killed 10 out of 11 crew members, 72 out of 76 passengers on board and 3 people on the ground died, including a famous Brazilian actress Leila Diniz at age 27. With 16 of the dead were Americans. Japanese investigators claimed a false glide path signal was responsible for the descent into terrain, while Indian investigators claimed it was caused by the JAL crew's disregard of laid down procedures and the abandonment of all instrument indications without properly ensuring sighting of the runway.
On 24 September 1972, Haruna, Japan Airlines Flight 472 operated by a Douglas DC-8 en route to Bombay landed at Juhu Airport runway 08, instead of Bombay Airport runway 09. The aircraft overran the runway through a ditch. The visibility at the time was 2.5 km (1.6 mi), decreasing to 1.5 km (0.93 mi). There were no injuries reported, but the aircraft was written off.
On 28 November 1972, Hida, Japan Airlines Flight 446 operated by a Douglas DC-8 from Tokyo to Moscow, climbed to 100 m (330 ft) with a supercritical angle of attack. The aircraft lost height, hit the ground and burst into flames. Nine of the 14 crew members and 52 of the 62 passengers died in the accident. The probable cause was "the supercritical angle of attack was caused by either an inadvertent spoiler-extension in flight, or a loss of control following a number one or two engine failure (due to icing)".
On 23 July 1973, Japan Air Lines Flight 404 operated by a Boeing 747-200B was hijacked by 4 men and a woman, shortly after leaving Amsterdam. An accidental explosion of the explosive device the woman hijacker was carrying occurred and she was killed. The aircraft was destined for Anchorage but was landed at Dubai and later took off for Damascus and Benghazi. Eventually, all the passengers and crew members were released and the aircraft was blown up.
On 12 March 1974, a Japan Airlines Boeing 747 was hijacked at Naha Airport. The hijacker demanded money, but the aircraft was stormed and the hijacker was arrested.
In February 1975, a Japan Airlines flight from Tokyo to Paris, making fuel stops in Anchorage and Copenhagen, had 196 passengers and one stewardess, out of 343 on board, fell ill with food poisoning, 143 of whom were seriously ill enough to need hospitalising when the plane reached Copenhagen, 30 of those critically ill. The source of the food poisoning was ham contaminated with Staphylococci from the infected cuts on the fingers of a cook in Anchorage. The ham was used in omelettes which were stored at a high temperature on the plane instead of being chilled, allowing time for the bacteria to multiply and produce an exotoxin that is not destroyed by cooking. The head of Japan Airlines catering service in Anchorage committed suicide shortly afterwards and was the only fatality of the incident. It was only luck that the pilots did not eat the omelettes (their body clocks were not in the right time zone for breakfast) and become incapacitated, leading some airlines to forbid pilots eating certain foods on the passenger menu.
On 9 April 1975, Japan Airlines Flight 514 operated by a Boeing 747SR was hijacked at Tokyo International Airport. The hijacker demanded money, the aircraft was subsequently stormed and the hijacker was arrested.
On 16 December 1975, Japan Airlines Flight 422 operated by a Boeing 747-200B (JA8122) slid off the north side of the east–west taxiway at Anchorage International Airport during taxi for a takeoff on runway 06R. The aircraft weathercocked about 70 degrees to the left and slid backward down a snow-covered embankment with an average slope of -13 degrees. The aircraft came to a stop on a heading of 150 degrees on a service road about 250 ft (76 m) from, and 50 ft (15 m) below, the taxiway surface.
On 5 January 1976, Japan Airlines Flight 768 operated by a Douglas DC-8 was hijacked at Manila Airport. There were two hijackers and they surrendered.
On 13 January 1977, Japan Airlines Cargo Flight 1045, a Douglas DC-8freighter stalled after lift off from Anchorage International Airport and crashed 300 m (980 ft) past the runway. The aircraft was on a non-scheduled operation and all five occupants on board, including three crew members and two passengers, were killed. The aircraft began takeoff at the wrong position on the runway and his decision was not questioned by his fellow crew members. The captain's initial blood alcohol level was 298 mg (4.60 gr); 100 mg (1.5 gr) was the legal intoxication limit for the state of Alaska. The probable cause was "a stall that resulted from the pilot's control inputs aggravated by airframe icing while the pilot was under the influence of alcohol. Contributing to the cause of this accident was the failure of the other flightcrew members to prevent the captain from attempting the flight".
On 28 September 1977, Japan Airlines Flight 472 operated by a Douglas DC-8 was hijacked by the JRA. The aircraft was en route from Paris to Tokyo with 156 people on board, made a scheduled stop in Bombay. Shortly after taking off from Bombay, five armed JRA members hijacked the aircraft and ordered to be flown to Dacca, Bangladesh. At Dacca (now Dhaka), the hijackers took the passengers and crew hostage, demanding $6 million and the release of nine imprisoned JRA members. A chartered JAL flight carried the money and six of the nine imprisoned JRA members to Dacca, where the exchange took place on October 2. The hijackers released 118 passengers and crew members, and all remaining hostages were freed later.
On 2 June 1978, Japan Airlines Flight 115 operated by a Boeing 747SR suffered a tailstrike while landing at Osaka; two passengers were seriously injured and another 23 suffered minor injuries. Although the aircraft was repaired in June and July 1978, it was lost in 1985 in the crash of Flight 123.
On 9 February 1982, Japan Airlines Flight 350 operated by a McDonnell DouglasDC-8 was on scheduled passenger flight from Fukuoka to Tokyo. The aircraft crashed on approach into the shallow water of Tokyo Bay, 510 m (1,670 ft) short of the runway 33R threshold. The nose and the right hand wing separated from the fuselage. Among the 166 passengers and 8 crew, 24 passengers were killed. The report shows that the captain had experienced some form of a mental aberration. He was prosecuted, but he was found not guilty by reason of insanity.
On 17 September 1982, Japan Airlines Flight 792 operated by a McDonnell DouglasDC-8 took off from Shanghai at 13:57. Nine minutes later, the crew heard a noise coming from the lower middle part of the aircraft. This was immediately followed by a hydraulic low level warning; a hydraulic reservoir air low pressure warning; a complete loss of hydraulic system pressure; abnormal flap position indications; and a complete loss of air brake pressure. The flight crew decided to return to Shanghai for an emergency landing on runway 36. The aircraft overran the runway and came to a rest in a drainage ditch.
On 17 November 1986, The crew of Japan Airlines Cargo Flight 1628, operated by a Boeing 747-200F, while en route to Tokyo, claimed to have spotted two Unidentified Flying Objects (UFO) at the Reykjavik to Anchorage section of the flight. They both had two rectangular arrays of nozzles / thrusters. When the UFOs were closer to the aircraft, the crew felt the heat coming from the nozzles / thrusters. They requested the air traffic controller in Anchorage, Alaska to send other close flights to witness the UFOs. However, a United Airlines flight came near the scene, but the crew did not report anything near Flight 1628. The unusual sight was for just under an hour and it ended near Denali.
On 2 October 1991, a Japan Airlines Boeing 747-200B was climbing through FL165 when the force from a hot liquid released from a burst pipe in the pressurization system, and blew a 100 cm × 70 cm (3.3 ft × 2.3 ft) hole in the fuselage beneath the port wing. The captain dumped fuel and returned safely to Tokyo.
On 31 March 1993, Japan Airlines Cargo Flight 46E, a Boeing 747-100 operated by Evergreen International Airlines, experienced severe turbulence at an altitude of about 2,000 ft (610 m) after departure about 12:24 local time, resulted in dynamic multi-axis lateral loadings that exceeded the ultimate lateral load-carrying of the number two engine pylon. This caused the number two engine to separate from the aircraft; the number one engine was maintained at emergency/maximum power and the aircraft landed safely back at Anchorage International Airport at 12:45.
On 8 June 1997, Etupirka, Japan Airlines Flight 706, operated by a McDonnell Douglas MD-11 from Hong Kong to Nagoya, descended through approx. 17,000 ft (5,200 m) over the Shima Peninsula for an approach to Nagoya. It then experienced abrupt and abnormal altitude changes, which injured five passengers and seven crew members. The captain was indicted for an alleged error in piloting the MD-11 aircraft, and then blamed for the death of a cabin crew member 20 months after the incident. The Nagoya District Court later acquitted the 54-year-old captain, Koichi Takamoto, on 31 July 2004.
On 28 October 2018, Japan Airlines pilot Katsutoshi Jitsukawa, 42, was arrested at Heathrow Airport for being under the influence after failing a breath test. He pled guilty to exceeding the alcohol limit on 1 November.
On December 4, 2020, a Boeing 777-200 operating JL904 from Okinawa to Tokyo Haneda suffered a fan blade failure in one of its two PW4084 engines. None of the 189 occupants on board were injured in the incident.