Record heavy rain forced the evacuation of thousands of people across parts of northern Japan as rivers burst their banks washing away bridges and cars, officials and media reports said Friday.

At least one person was killed and four missing after the downpours in Yamagata and Akita prefectures on the main island of Honshu.

A man in his 60s was missing after a landslide at roadworks in Yuzawa City, while an 86-year-old man was unaccounted for after last being seen on a river bank in Akita City, police told AFP.

One body was found in Akita City, media reports said.

A local official told AFP in Yamagata, where two rivers burst their banks, that "three people, including two police officers who were on a mission searching for a missing man, are unaccounted for".

Two parts of Yamagata prefecture recorded the most rain in 24 hours since records began in 1976, the Japan Meteorological Agency (JMA) said Friday.

Shinjo recorded 389 millimetres (15 inches) and Sakata 289 millimetres.

Footage showed raging brown waters sweeping away several vehicles including a police car.

Authorities issued evacuation advisories to more than 200,000 people, the fire and disaster management agency said.

At least 4,000 people evacuated to shelters, public broadcaster NHK reported.

About 3,060 households were without power, 1,100 had no running water.

Some motorways were closed in the area and Shinkansen bullet trains suspended operations, government spokesman Yoshimasa Hayashi told reporters.

The military was sent to Yamagata to join rescue activities carried out by police and fire department officials, he said.

Japan's weather agency this week issued its highest emergency alert for heavy rain for Sakata and Yuza in Yamagata prefecture.

It later downgraded the warning by one notch in the country's five-tier warning system, but called for the public to stay vigilant for potential landslides and flooding.

The JMA forecasts 100 to 200 millimetres of rain per day will continue for the next three days.