Japan is preparing for its strongest typhoon of the year, with authorities reporting landslide deaths, advising tens of thousands of people to evacuate and issuing the highest warning level for wind and storm surges on the main southern island of Kyushu.

“Typhoon Shanshan is expected to approach southern Kyushu with extremely strong force through Thursday and it may make landfall,” chief cabinet secretary Yoshimasa Hayashi told reporters. “It is expected that violent winds, high waves and storm surges at levels that many people have never experienced before may occur.”

The approach of the storm, packing gusts of up to 252km/h (157mph) and already bringing widespread heavy rain, prompted auto giant Toyota to suspend production at all 14 of its factories.

Three members of a family died after a landslide buried a house in Gamagori, a city in central Aichi prefecture, Japan’s Kyodo news agency reported early on Thursday, citing local government officials.

The deceased included a couple in their 70s and a son in his 30s, while two adult daughters in their 40s were injured, the agency said.

For southern Kyushu the Japan Meteorological Agency (JMA) predicted 1,100mm (43in) of precipitation in the 48 hours to Friday morning, around half the annual average for the area comprising Kagoshima and Miyazaki regions.

The JMA also issued its highest “special warning” for violent storms, waves and high tides in parts of the Kagoshima region, with authorities there advising 56,000 people to evacuate.

Video on public broadcaster NHK TV showed roof tiles being blown off houses, broken windows and felled trees.

“Our carport roof was blown away in its entirety. I wasn’t at home when it happened, but my kids say they felt the shaking so strong they thought an earthquake happened,” one resident in Miyazaki told NHK. “I was surprised. It was completely beyond our imagination,” she said.

The warnings indicate the “possibility that a major disaster prompted by [the typhoon] is extremely high,” Satoshi Sugimoto, chief forecaster of JMA, told a news conference.

Japan Airlines cancelled 172 domestic flights and six international flights scheduled for Wednesday and Thursday, while ANA scrapped 219 domestic flights and four international ones across Wednesday, Thursday and Friday.

The cancellations affected about 25,000 people.

Kyushu Railway said it would suspend some Shinkansen bullet train services between Kumamoto and Kagoshima Chuo from Wednesday night and warned of further possible disruption. Trains between Tokyo and Fukuoka, the most populous city on Kyushu, may also be cancelled depending on weather conditions this week, other operators said.

Shanshan comes in the wake of Typhoon Ampil, which disrupted hundreds of flights and trains this month. Despite dumping heavy rain, it caused only minor injuries and damage.

Ampil came days after Tropical Storm Maria brought record rains to northern areas.

Typhoons in the region have been forming closer to coastlines, intensifying more rapidly and lasting longer over land due to the climate crisis, according to a study released last month.

Human-caused climate breakdown has increased the occurrence of the most intense and destructive tropical cyclones (though the overall number per year has not changed globally). This is because warming oceans provide more energy, producing stronger storms.

Extreme rainfall from tropical cyclones has increased substantially, as warmer air holds more water vapour. For example, the amount of rainfall produced by Hurricane Harvey in Texas in 2017 would have been all but impossible without the record-warm ocean water in the Gulf of Mexico.

Coastal storm surges are also higher and more damaging due to the sea level rise driven by climate breakdown. For example, the devastating storm surge from Typhoon Haiyan, which hit the Philippines in 2013, was about 20% higher due to human-caused climate breakdown.