The transport ministry slapped All Nippon Airways Co. with a severe warning Tuesday after a plane pushed back for takeoff with a seat-less passenger standing in the aisle.
The incident last month involved ANA Flight 256, a Boeing 777 service from Fukuoka to Tokyo's Haneda airport.
All 405 passenger seats were full, and a boarding-pass error had put one too many people aboard, according to the Ministry of Land, Infrastructure, Transport and Tourism.
A father and son checked in for the flight and went aboard using the same QR code by mistake.
The son downloaded his father's pass and passed through the boarding gate first. When the father swiped his phone the reader delivered a "re-entry" alert. Security staff thought the man had simply touched it twice and after checking his identity they allowed him through.
Because the system had no record of the son's boarding pass having been used, a flier on a waiting list was invited to board, and the father found himself without a seat.
Right after the aircraft left the gate at Fukuoka Airport, a cabin attendant found a man standing in an aisle and the plane returned. The man and his son disembarked and the plane departed after a delay of around 45 minutes.