The 6.1 quake collapsed more buildings in Ojiya and smoke could be seen in the city of Nagaoka in the mostly rural Niigata area, 250km north of Tokyo.
The latest tremor hit at 10.40am local time (0140 GMT) and was also felt strongly in Tokyo, but there were no reports of damage in the capital.
Saturday's earthquake, with a magnitude of 6.8, was Japan's deadliest since a 7.2 magnitude quake killed more than 6400 people in the western city of Kobe in 1995.
As many as 100,000 survivors of Saturday's quake, many of them elderly, are still in makeshift shelters, facing another day of stress and fatigue, raising fears that the death toll could rise.
A man in Ojiya collapsed, apparently after suffering a stroke, and was taken to hospital by helicopter, national broadcaster NHK said. Four others were injured, media said.
The elderly have proven to be most
at risk from continued tremors
About 1000 people had been evacuated from the main train station in Nagaoka, which has a population of about 200,000.
Many of the injured in Saturday's quake and the subsequent series of big aftershocks were elderly people who had suffered heart attacks, strokes or shock, and authorities were concerned that cold weather and fatigue could claim more lives.
Rescue workers found a family of three - a mother and her two children - still alive on Wednesday after surviving for four days under a landslide, officials said.
The two children - Mayu Minagawa, three, and Yuta Minagawa, two - were already rescued, and workers said they heard the voice of their mother, Takako Minagawa, 39, from under the rubble, said Niigata Prefectural government spokesman Kiyokazu Urabe.
The focus of Wednesday's tremor was 10km below the surface of the Earth, the Japan Meteorological Agency said, adding that there could be more large aftershocks.
More to come?
John Bellini, a geophysicist at the US Geological Survey National Earthquake Information Center in Golden, Colorado, said the initial quake had been followed by more large aftershocks than was usually the case. "These could go on for days or weeks," he said.
The new earthquake measured a "lower 6" on the Japanese scale of 7, which reads ground motion. Typically quakes of that intensity make it difficult to keep standing and gas pipes and water mains are likely to be damaged.
The magnitude of the earthquakes was measured according to a technique similar to the Richter scale, but adjusted for Japan's geological characteristics. The US Geological Survey rated the latest quake at magnitude 5.7 on its scale.
Earthquakes are common in Japan, one of the world's most seismically active areas. The country accounts for about 20% of the world's earthquakes of magnitude 6 or greater.