A strong earthquake with a magnitude of 5.6 shook rural Niigata prefecture, about 250km north of Tokyo, early on Monday, two days after the first big tremor that killed at least 25 people and injured more than 2700.
Japan's meteorological agency said an increase in aftershocks meant there was a 40% chance of an earthquake of magnitude 6.0 or greater in the area in the next week.
Saturday's initial earthquake had a magnitude of 6.8. It was the deadliest in the country since the 1995 Kobe earthquake which killed more than 6400 people.
Fear of landslides
Rain and falling temperatures prompted fears of more landslides and of a cold and bitter night for those homeless or too frightened to return to their houses.
The meteorological agency warned that even relatively light rain might set off landslides and the authorities in Ojiya, one of the worst affected towns, urged more people to evacuate.
Many survivors were too scared
to return to their homes
"Landslides are a worry," said a Niigata government official. "In addition, it is already very cold at night for people who are camped outside and if it rains this will get even worse."
Tens of thousands of people have already spent two nights in evacuation centres or in the open as the temperature fell below 10C.
Supplies running out
Some slept in their cars with the engines running, but many petrol stations had closed after running out of supplies.
"There has been big damage to lifelines of electricity, gas and water and many people are at evacuation centres, unable to go home," Chief Cabinet Secretary Hiroyuki Hosoda said.
"The government is making every effort ... for disaster relief and reconstruction so that those affected can return to their livelihoods with peace of mind," he said, adding that the government would approve extra spending if needed.
"I have no food. I have nothing to drink. I have no change of clothes for my children. But I'm relieved"
Rescued young woman
The tremors follow a record 10 typhoons to hit Japan this year, including one that killed at least 80 people last week.
Military helicopters airlifted around 2000 residents of the village of Yamakoshi, where many had been stranded by landslides.
"I have no food. I have nothing to drink. I have no change of clothes for my children. But I'm relieved," said a young woman after being rescued.
Can't do business
As of Monday evening, the number of people evacuated had risen to nearly 98,000, Japanese media said. Tohoku Electric Power struggled to restore electricity to the area, where 57,000 households were still without.
About 2800 homes were completely or partly destroyed and more than 1000 other buildings damaged, public broadcaster NHK said. Telephone services were disrupted, train rails twisted and highways severely damaged.
Rail tracks and highways were
"There's no way I can do business and I haven't a clue when I'll be able to," said a middle-aged man cleaning up around the building that had housed his garage before it slid down a riverbank near Ojiya.
Since the Kobe earthquake, the authorities have improved their rescue work, experts said. "The response this time wasn't perfect, but it definitely was much better," said Takehiko Yamamura, head of the private Disaster Prevention System Institute.
There were no reports of significant damage to industry in the region, which includes chemical and textile manufacturing as well as electronics and food processing.
But some factories had halted operations and damage to roads and railways raised concerns about distribution bottlenecks.