A computer system malfunction forced Japan's All Nippon Airways to cancel more than 100 domestic flights on Tuesday, affecting some 16,000 travellers, the carrier said.

ANA ground staff at Tokyo's Haneda airport apologised to stranded passengers, some who could be seen making mobile phone calls and sending text messages while children sat on the floor of the crowded terminal hall playing video games.

Passengers lined up patiently at counters to arrange new reservations for later flights as the airline's reservation and check-in hall overflowed with inconvenienced travellers.

ANA said it spotted something wrong at about 8:20 am (local time) Tuesday and though the problem was largely resolved about three hours later at least 127 domestic flights were cancelled by afternoon.

The trouble stopped reservations, ticket sales and boarding procedures, affecting the travel plans of at least 16,100 passengers at 49 airports throughout Japan as of 3 pm, the airline said.

"The boarding procedure system recovered at 11:30 am, but we still have trouble with reservations and ticket sales," spokeswoman Natsuki Uota said Tuesday afternoon.

The airline was investigating what caused the system to go down.