Typhoon Lan made landfall in Japan early Tuesday, bringing violent gusts and downpours that have already caused rivers to surge and prompted landslide warnings.

Lan crossed the coast of the main island of Honshu shortly before 5 am (2100 GMT) in Wakayama prefecture, some 600 kilometres (375 miles) west of Tokyo, the Japan Meteorological Agency said.

The system was set to spend all of Tuesday sweeping over the region, which includes the commercial hubs of Osaka and Kobe before moving out to the Sea of Japan.

"Please exercise extreme caution against landslides, surging water in low-lying areas, swollen and flooded rivers and violent winds," the agency said in a warning issued for numerous areas.

The system has prompted the cancellation of hundreds of flights and trains, including high-speed "Shinkansen" bullet train services that link the region with capital Tokyo.