Six people died and three others were missing after the “heaviest rain ever” triggered floods and landslides in south-west Japan.

The Japan meteorological agency warned residents in Kyushu – one of the country’s four main islands – to stay alert for more landslides, a common hazard in mountainous areas after heavy rainfall.

However, the agency on Tuesday downgraded an earlier special warning for heavy rain covering more than 1.7 million people in northern parts of the island.

Japan has been hit by unusually heavy rain and powerful typhoons in recent years, raising fears about its vulnerability to the climate crisis.

“This is the heaviest rain ever experienced” in the region, said Satoshi Sugimoto, a meteorological agency official. “The situation is such that lives are in danger and their safety must be secured.”

The chief cabinet secretary, Hirokazu Matsuno, said up to six people were thought to have died as a result of heavy rain that caused rivers to burst their banks and disrupted to bullet train services, as well as cutting off roads and water supplies.

Flood debris in Kurume, Fukuoka prefecture, Kyushu island. Photograph: Kazuhiro Nogi/AFP/Getty Images

The prime minister’s office said a taskforce had been set up to coordinate a response.

“We have received reports that several rivers have flooded … and that landslides have occurred in various parts of the country,” Matsuno told reporters.

“The government is doing its best to get a complete picture of the damage and taking measures while putting people’s lives first.”

A 77-year-old woman was confirmed dead after she and her husband were found trapped inside their house, which had been engulfed in mud, in Fukuoka prefecture, local authorities said, adding that the husband had survived.

Three other Fukuoka residents died, including one whose car had been washed away by a flooded river.

The city of Kurume saw precipitation of 402.5mm in the 24 hours to 4pm on Monday – the highest ever recorded there – the meteorological agency said.

A mudslide in the city hit seven houses, burying 21 people. Six were able to escape, while workers extracted nine alive and were working to remove five others. A man in his 70s was later confirmed dead.

The body of another man was found next to rice fields near a flooded river, according to the Yomiuri Shimbun newspaper and public broadcaster NHK.

“The rain and gusts of wind were very, very strong, and there was lightning,” said Takashi Onizuka, a 62-year-old resident of a town near Kurume. “It was so horrible.”

While Tokyo experienced blistering heat on Tuesday, other parts of the country bore the brunt of the annual rainy season.

Scientists say global heating is increasing the risk of heavy rain in Japan. The weather agency said it had already been raining for more than a week in parts of northern Kyushu.

Officials in the city of Asakura said they believed the rain had peaked, but warned there was still a risk of flooding.

“Water levels in rivers are rising so we are staying vigilant against the possibility of overflowing,” said Takaaki Harano, a local official.

Landslides represent a serious risk in Japan, where many homes are built on flat land at the foot of hills and mountains.

In 2021, a landslide in the hot spring resort of Atami killed 27 people; and in 2018, floods and landslides killed more than 200 people in western Japan during the rainy season.