Sanjo City in Niigata, about 200km north of Tokyo, advised all 104,000 residents to go to flood evacuation centres, Jiji Press news agency said.
Rain had topped half a metre at several points since Wednesday, it said.
"There are no immediate reports of injuries or deaths, but we urge our citizens to evacuate to the designated shelters as soon as possible and stay on alert," said Ayaka Hoshi, a Sanjo City spokeswoman.
In the prefectural capital Niigata, about 72,000 people were asked to evacuate.
In neighbouring Fukushima prefecture, the town of Tadami advised all its residents, about 4900 people, to evacuate, Jiji said. Two men, both in their 60s, were missing, it said.
Police in Niigata said three members of a family in Tokamachi city had been swept away in a river. Two were recovered safely but the third, a 93-year-old woman, was missing, the agency said.
Two men were missing in other parts of Niigata prefecture.
Officials had requested the Self-Defence Force dispatch troops to join the search for missing people and help those stranded by mudslides and floods, Jiji and Kyodo News said.
More than 70,000 homes and buildings in Niigata and Fukushima prefectures were hit by power blackouts, Kyodo reported, with many houses flooded.
Fukushima is home to the Fukushima Daiichi nuclear power plant which was crippled by the massive March 11 earthquake and tsunami.