Three others were missing in Niigata and Fukushima, the latter of which was ravaged on March 11 by a 9.0-magnitude earthquake and tsunami which knocked a nuclear power plant out of control.

A strong 6.4-magnitude quake, which seismologists said was an aftershock of the massive tremor, struck off Fukushima's coast early Sunday, injuring seven people.

Thousands remained sheltered at evacuation centre to avoid floods from the rain storm since Wednesday following torrents that killed at least 59 in South Korea last week.

Local governments in Niigata and had issued guidance since Friday to more than 60,000 people to flee their homes, the national Fire and Disaster Management Agency said.

Several thousands were estimated to remain sheltered in Niigata early Sunday, an official at the Niigata prefecture office said. He could not immediately confirm how many people had actually been evacuated.

In Fukushima, 1,020 were sheltered as of late Saturday, the Jiji Press news agency said.

The Fire and Disaster Management Agency said 2,278 houses had been flooded.

"The rain reached a peak in Niigata and Fukushima yesterday. It is still raining hard intermittently in limited areas," Japan Meteorological Agency official Kenji Okada said. "Its focus shifted slightly south."

In Niigata, the body of a third victim, a 63-year-old man, was recovered early Sunday. "He was sandbagging a levee when he was washed away into a river," a prefecture police official told AFP by telephone.

Two persons were found dead in Niigata late Saturday after they fell into rivers while driving cars.

Copyright AFP (Agence France-Presse), 2011