• ANA's first crash occurred in 1958 when a Douglas DC-3 JA5045 operating as Flight 025 crashed.
• In 1958, dynamite was planted in a Douglas DC-3 by Akira Emoto, a candy salesman, as part of a suicide plan. Emoto killed himself by leaping from the aircraft and the bombs failed to detonate.
• In 1960, a Douglas DC-3 JA5018 was damaged beyond economic repair shortly after landing at Nagoya-Komaki International Airport when a JASDF F-86 Sabre fighter crashed into the aft fuselage and tail section while attempting to take off. 1 of 3 crew members, and 2 of 33 passengers were killed. The pilot of the F-86D Sabre also survived.
• On 12 June 1961, Vickers Viscount G-APKJ was damaged beyond economic repair when the starboard undercarriage collapsed following a heavy landing at Osaka Itami Airport.
• On 19 November 1962, Vickers Viscount JA8202 crashed at Nagoya while on a training flight, killing all four people on board.
• On 4 February 1966, Flight 60, operated by Boeing 727 JA8302, was landing at Tokyo Haneda Airport when it crashed into Tokyo Bay with the loss of all 133 passengers and crew.
• On 13 November 1966, Flight 533, a YS-11 crashed in Matsuyama. All 50 aboard the aircraft were killed.
• On 30 July 1971, Flight 58, a Boeing 727, registration JA8329, collided with a JASDF F-86 Sabre fighter stationed at Matsushima Air Base.
• On 22 June 1995 a man calling himself "Fumio Kujimi" and registered with ANA as "Saburo Kobayashi" hijacked Flight 857, a Boeing 747SR, after it took off from Tokyo. The plane landed in Hokkaidō and police stormed the aircraft, arresting the hijacker Police stated that the hijacker was 53-year-old Fujio Kutsumi; he had demanded the release of Shoko Asahara. The hijacking incident lasted 16 hours.
• In 1999, a man hijacked Flight 61 and killed the captain. He was subdued by other crew members, and no passengers or other crew were killed or injured.
• On 6 September 2011, Flight 140, an All Nippon 737-700 traveling from Naha to Tokyo with 117 passengers and crew, banked over 90 degrees in mid-air and rapidly descended as the First Officer accidentally hit the rudder trim switch instead of the door unlock button as the captain returned from the lavatory. The First Officer eventually regained control and levelled the plane. There were minor injuries to two flight attendants.
• On 8 December 2012 an ANA Boeing 737 slid 80 meters off the end of the runway at Shonai Airport when landing during a snowstorm. There were no injuries to passengers and crew and the aircraft was not seriously damaged.
• On 16 January 2013, Flight 692, a Boeing 787 flying from Yamaguchi Ube Airport to Tokyo Haneda Airport reported a battery problem while climbing to FL330. The pilots made an emergency landing at Takamatsu Airport. No casualties were reported during the evacuation. However, after this incident, all 787s were subsequently grounded by respective aviation authorities until the battery issue was resolved.