The strongest typhoon to hit Japan in 25 years made landfall, the country's weather agency said, bringing violent winds and heavy rainfall that prompted evacuation warnings.

Typhoon Jebi, packing winds of up to 216km/h, made landfall around midday in western Japan near areas still recovering from deadly record rains earlier this summer.

Incredible footage from the storm showed buildings being damaged, fierce wind and rain and a truck being blown over by the ferocious gales.

Prime Minister Shinzo Abe urged people to "evacuate early" and ordered his government to take all necessary measures to protect residents.

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Japan's weather agency has issued warnings about possible landslides, flooding and violent winds, as well as high tides, lightning and tornadoes in a swath of western Japan including the major cities of Osaka and Kyoto.

With winds of up to 162km/h at its centre, Jebi is classed as a "very strong" typhoon, the weather agency's chief forecaster Ryuta Kurora said.

"This is (the strongest) since 1993."

Evacuation advisories were issued for more than 300,000 people as the wind and rain from Typhoon Jebi began to intensify on Tuesday afternoon. Most of those advised to leave their homes and head to 1500 temporary shelters were in the western port city of Kobe.

As it made its way north from the southern island of Okinawa, Jebi was already causing widespread disruption to flights and public transport. Nearly 600 domestic and international flights were cancelled, along with scores of ferries and trains, the public broadcaster NHK said.

In the hours before the storm made landfall, Shikoku, one of four Japanese main islands, was already experiencing "violent storms and the storms will get stronger and stronger," he added.

As the storm approached, Abe called a disaster response meeting and cancelled a trip to western Japan.

"I urge the Japanese people to take action to protect your lives, including preparing and evacuating early," he said.

High waves hit breakwaters at a port of Aki, Kochi prefecture, Japan. Photo / AP
High waves hit breakwaters at a port of Aki, Kochi prefecture, Japan. Photo / AP

The typhoon is the 21st of the season. After hitting western Japan, it is set to speed up further as it passes over the main island of Honshu and into the Sea of Japan, where it will weaken.

While Tokyo will be spared the worst of the storm, authorities have warned of very strong winds and heavy rain even in the capital.

West Japan Railway Co. has begun halting local trains and plans to stop all local services in the area's three main cities. Shinkansen high-speed trains between Osaka and Hiroshima were set to be cancelled from mid-morning, with JR West warning it might not be able to restart services all day. Services from Tokyo to Osaka were running reduced operations.

The Universal Studios Japan theme park, one of Osaka's main tourist draws, will shut down for the entire day. Authorities called on residents to avoid any unnecessary trips outside.

The typhoon may also bring further downpours to areas that were devastated by sudden rainfall in early July that killed more than 200 people. Jebi is predicted to bring heavy rains tomorrow.

- Bloomberg

A couple watches waves hitting a coast of Shirahara town, Wakayama prefecture, central Japan. Photo / AP
A couple watches waves hitting a coast of Shirahara town, Wakayama prefecture, central Japan. Photo / AP
High waves hit breakwaters at a port of Aki, Kochi prefecture, western Japan from powerful Typhoon Jebi. Photo / AP
High waves hit breakwaters at a port of Aki, Kochi prefecture, western Japan from powerful Typhoon Jebi. Photo / AP