Two women in their 80s died when their homes collapsed due to the magnitude 6.8 tremor, centred in Niigata prefecture some 250 km (155 miles) northwest of Tokyo, Japanese media said.
Kyodo news agency said a 79-year-old woman was also killed. Earlier reports of a fourth death were later withdrawn.
"It was too strong to stand. Some people got under tables, others immediately went outside," said police officer Masao Honma in Kashiwazaki City, near the focus of the quake.
"It's really rough," Honma told Reuters by phone.
Houses, many wooden with traditional heavy tile roofs, were flattened, a temple roof caved in and roads cracked in the quake, which was centred in the same northwestern area as a tremor three years ago that killed some 65 people.
Firemen and troops worked to rescue a woman after her voice was heard from under collapsed house, public broadcaster NHK said.
Hours after the initial quake, an aftershock with a preliminary magnitude of 5.6 jolted the area, sending more roof tiles tumbling and making it hard for some people to stand.
NHK said that more than 1,000 people had fled their homes for the nearly 100 evacuation centres that a Niigata Prefecture official said were being set up, and troops and extra emergency teams were being sent to help with rescue and relief efforts.
Buildings swayed as far away as Tokyo, and nuclear power reactors in Niigata prefecture automatically shut down for checks but there were no radiation leaks reported.
A fire in an electrical transformer at the Kashiwazaki Kariwa nuclear power plant -- the world's largest -- was quickly extinguished but it was unclear when Tokyo Electric Power Co (TEPCO) could restart three power units there, said Yoshinobu Kamijima, a company spokesman.
