The storm, named Krosa, is expected to churn slowly over western parts of the country, potentially affecting millions of people returning to major cities from their hometowns after the traditional "Obon" summer holidays.
Japan Airlines scrapped 62 domestic flights to and from airports in southern Japan for Wednesday.
"All the flights from and to Miyazaki and Tanegashima airports have been cancelled and partially for Amami airport," a spokesman told AFP.
All Nippon Airways meanwhile cancelled 34 flights for Miyazaki airport. Both airlines said they would decide later how many flights they will cancel for Thursday, when the storm is forecast to make landfall.
Meanwhile, West Japan Railway announced the cancellation of Thursday's shinkansen bullet train service between Osaka and southwestern Japan.
Krosa, which is packing maximum gusts of 144 kilometres (90 miles) per hour, was expected to hit the southwestern Shikoku island on Thursday before moving across western Japan, the Japanese Meteorological Agency said.
The agency warned of the risk of landslides and flooding due to heavy rain.