Homeless residents huddled in blankets and started small fires in front of public shelters, shocked from the night before when quakes left at least 19 dead and injured nearly 900 more.
While Japan is accustomed to earthquakes, the epicentres are often in the ocean and inflict limited damage.
But starting just before 6.00pm (0900 GMT) on Saturday in Niigata Prefecture, plates and televisions came crashing down after an initial tremor of 6.8 on the Richter scale and hundreds of aftershocks.
"I jumped under my dining table but everything from the walls fell down and bowls and dishes were all around my feet," said one woman in her fifties in the town of Ojiya, 200km northwest of Tokyo.
"I ran outside and when I looked at the buildings they were shaking like pudding," a man in his 20s in nearby Mitsuke told the Japan Broadcasting Corporation (NHK).
The quakes followed the worst typhoon season on record, including the deadly Typhoon Tokage which struck on Wednesday. It killed 79 people and left 12 missing.
Happy to be alive
"Everything in my house, including the television and lights, fell and was smashed," one man in his thirties told NHK. "I'm just happy I have my life."
As two powerful aftershocks hit on Sunday, the Defence Agency sent 230 personnel in vehicles and helicopters to rescue stranded and injured residents and provide clean water.
About 58,700 people were evacuated from their homes.
The initial tremor measured 6.8
on the Richter scale
One helicopter touched down in Ojiya to help move 50 people and four injured from a rural area to an elementary school and hospital.
First ever derailment
"We're all right, we're all right," one elderly woman told NHK as she boarded a helicopter. Another elderly woman with a cane was seen carried by a soldier as the helicopter waited nearby.
A high-speed bullet Shinkansen train was also derailed near the focus of the quake on Saturday, but no one among about 150 passengers was injured, rail operator JR East Japan said. It was the first bullet train derailment for any reason.
The Japanese Red Cross Society said it had sent 27 staff to hospitals and shelters in the area to help patients and distribute blankets, canned food, bread and soup.
About 170 of the injured had been assembled at the Nagaoka Red Cross Hospital. Most suffered from bruises, broken bones, and cuts and scratches.
"I ran outside and when I looked at the buildings they were shaking like pudding"
Witness told the Japan Broadcasting Corporation (NHK)
The Red Cross also planned to distribute three tons of emergency kits with medical supplies to provide 200 people with three days worth of supplies.
In the early morning, another 70 Red Cross staff were dispatched to the hospital to look after the mental and spiritual health of shaken victims.
The series of quakes was the deadliest since the 1995 earthquake measuring 7.3 on the Richter scale in Kobe, which killed 6433 people and injured 43,700, the Fire and Disaster Management Agency said.