Nearly 2,500 passengers of Japan Airlines Co. were affected due to an outage in its automated check-in system forced the airline to cancel 32 domestic flights.
Other domestic flights were also delayed by up to two and a half hours, according to Kyodo News.
The system was restored by 10am, and JAL is investigating the cause of the incident, which it says likely resulted from a network fault.
Issues with the check-in system began at around 6.50am, forcing passengers to complete the boarding process over the counter. Baggage check-in services were unaffected by the system failure.
Flight connections linking Tokyo with Fukuoka, and Osaka with Sendai were among those cancelled.