Typhoon Shanshan soaked large swathes of Japan with torrential rain on Friday, prompting warnings for flooding and landslides hundreds of miles from the storm's centre, halting travel services and shutting production at major factories.

At least four people have been killed and 99 injured in storm-related incidents in recent days, according to the disaster management agency.

In the southwestern region of Kyushu, where the storm that authorities say could be one of the strongest ever to hit the region made landfall on Thursday, residents were surveying the damage after a night of heavy rain and severe winds.

Yu Fukuda, 67, who runs a fish farm and adjoining restaurant in the resort town of Yufu in Oita prefecture said she arrived on Friday morning to find flood waters one-metre (3 ft) high had inundated the building.

"There were streaks on the windows and everywhere there were marks from mud and dirt, so I could tell how high the water had risen. I felt very sad," she told Reuters as her staff and relatives cleared the debris of fishing nets and dead fish.

"I wish the typhoon had just passed quickly, but it stayed around here for a long time," she said.

Bringing gusts of up to 50 metres per second (180 km per hour/112 mph), strong enough to blow over moving trucks, the typhoon was near the coastal city of Matsuyama in Ehime Prefecture at 3:45 p.m. (2345 GMT) and moving east, according to authorities.

Around 250,000 households in seven prefectures were without power in Kyushu on Thursday, according to Kyushu Electric Power Co., but many had seen services restored on Friday.

The warm and moist air flowing around the typhoon brought record-breaking levels of rain in some areas far from the main storm, which authorities say is concerning given its slower than expected movement across the country.

Notices advising residents to evacuate have been issued to more than 3.3 million people nationwide, mostly in the hard-hit Kyushu area and central and eastern regions including the capital Tokyo and nearby Yokohama. 

Authorities there warned of possible landslides and rivers bursting their banks due to the heavy rain.

Shizuoka, a major city in central Japan, has seen more than 500 millimetres of rain in the last 72 hours, the highest volume since the weather agency began collecting the data in 1976.

But, as of Thursday, only some 30,000 had been evacuated, mainly in Kyushu, disaster management minister Yoshifumi Matsumura said.

The storm is expected to approach the central and eastern regions, which includes Tokyo, at the weekend and into early next week, the weather agency said.

Toyota (7203.T), opens new tab has suspended operations in all of its domestic plants through Monday morning due to the storm. Other automakers Nissan (7201.T), opens new tab and Honda (7267.T), opens new tab, semiconductor firms Renesas (6723.T), opens new tab and Tokyo Electron (8035.T), opens new tab, and electronics giant Sony have also temporarily halted production at some factories.

Airlines, including ANA Holdings (9202.T), opens new tab and Japan Airlines (9201.T), opens new tab, have announced cancellations of hundreds of domestic and some international flights. Many ferry and rail services, including the bullet train between Tokyo and the central city of Nagoya, were suspended on Friday morning.

Lin Yue-Hua, a 60-year-old tourist from Taiwan, had her flight from Fukuoka back home cancelled on Thursday. She was told to book another flight but was struggling to make her way to the airport on Friday morning.

"We were very worried and upset because we didn’t know what to do," she told Reuters at a near-deserted train station on Friday morning after finding out that all rail services, including the subway to the airport, had been cancelled.

"We stayed one more day in Japan. Then we saw it in the news that our flight from Taiwan couldn’t land in Japan after flying around the area for about 40 minutes and it flew back to Taiwan. We have been busy trying to find our way home," she said.

Typhoon Shanshan is the latest harsh weather system to hit Japan, following Typhoon Ampil, which also led to blackouts and evacuations, earlier this month.