A typhoon-strength storm, with violent gusts up to 100 kilometers an hour were expected in the east of the country, including Tokyo.
Sustained winds of 90 kilometers per hour would be the strongest to hit the capital since 1959, when a storm hit Tokyo with winds of 97 km/h, data from the weather agency show.
As of mid-day Tuesday, 203 flights were already grounded nationwide. Japan Airlines cancelled 160 domestic flights, affecting 23,700 passengers, while international flights experienced minor delays.
All Nippon Airways cancelled 83 domestic flights, affecting 8,900 people.
East Japan Railways, which operates a vast train network in the eastern and northern regions, including Tokyo, cancelled a number of long-distance services.
The nation’s main bullet train, linking Tokyo and the western city of Osaka, was experiencing delays, but was running in the early afternoon.
Nissan ordered employees to leave work at 2 p.m. today to avoid the storm.
Spokeswomen for Toyota Motor Corp. and Honda Motor Co. said there were no plans to close factories early.