Three women found dead Wednesday brought the death toll from massive rain and floods that hit Niigata and Fukushima prefectures the previous day to six.
Four other people were listed as missing, local police said. The Meteorological Agency has meanwhile warned of more heavy rain in the area.
Some 14,000 residents took refuge at schools and other public facilities in Niigata Prefecture overnight, while efforts continued by boat and helicopter to rescue people trapped in their homes in flooded areas.