A glitch in Japan Airlines Co.'s weight management system led to the cancellation of 46 domestic flights to and from Tokyo's Haneda airport on Friday, affecting about 6,700 passengers, the company said.

The trouble occurred at around 7:50 a.m., prompting JAL to deploy an alternative system. The cause of the glitch, which was fixed by 9:40 a.m., remains unknown, the airline said.

The processing speed slowed significantly while the alternative system was used, JAL said.

A similar problem in JAL's weight management system occurred in June 2014, causing the cancellation of 174 domestic flights and inconveniencing 14,000 passengers.

JAL President Yoshiharu Ueki told reporters, "I offer a deep apology for causing so much trouble with the system glitch."

On March 22, a check-in system failure at 50 airports in Japan hit All Nippon Airways Co., affecting some 72,000 passengers.

At Haneda airport, frustrated passengers flocked to JAL service counters to seek information.

Noriyuki Takaki, 55, who was supposed to fly to Hiroshima in the morning for a business meeting in the afternoon, said, "ANA was hit by (similar system trouble) only recently. I have an impression that (airline computer) systems are too vulnerable."

"I wonder whether I should travel by shinkansen from now on," he said.

Transport minister Keiichi Ishii expressed regret over a series of system glitches affecting Japanese airlines. "I have been instructing (JAL) to look into the cause and impact of the trouble and serve customers attentively," the minister said at a news conference.