In a saga broadcast live on television, rescuers with shovels pulled Takako Minagawa, 39, and her two-year-old son from heaps of rocks and mud in Nagaoka, one of the cities worst hit by Saturday's quake.

The boy, Yuta, suffered no major injury except for a cut on his forehead and was heard muttering "Mama" to a nurse at Nagaoka Red Cross Hospital, hospital director Kenzo Kaneko said.

"He's with his father now and telling him he wants to drink water," Kaneko told a nationally televised press conference.

But he said the boy's mother was dead on arrival at the hospital.

The other child, a three-year-old girl called Mayu, remained trapped inside the car with her shoe wedged between the piles of rocks.

The dozen-strong relief team, dressed in orange protective suits, briefly suspended efforts to save the girl when night fell before resuming work, a spokesman for the prefecture said.

Rescuers do not know for sure whether she is still alive.

The car was buried by a landslide during the initial quake of 6.8 on the Richter scale Saturday and was not found until late Tuesday.

But rescue work had to wait until daylight on Wednesday while fresh aftershocks continued. Specialists from Tokyo's fire department located the three through advanced instruments including fibrescopes.

With the mother's death, 32 people are known to have died since Saturday's initial tremor hit the Niigata prefecture 200 kilometres (125 miles) northwest of Tokyo, some from stress amid the hundreds of aftershocks.

Quake survivors Wednesday experienced another tremor measuring 6.1 on the Richter scale which was powerful enough to sway buildings in Tokyo.

The tremor sent quake victims in shelters hurriedly lying down on the floor for their safety. About 86,000 people are still lodged in hundreds of shelters across Niigata province.

Public broadcaster NHK said 20 people were injured in the latest tremor.

In Ojiya city, the hardest hit by the initial quake, an apartment building collapsed and damaged an adjacent clinic but two residents inside were rescued unharmed, a municipal official said.

The latest tremor also triggered at least one landslide and violently shook elevated rail tracks of Japan's bullet train -- which was derailed for the first time in its 40-year history by Saturday's quake.

Workers who had been trying to lift derailed carriages were seen scurrying back as they shook with the new tremor. The Niigata train station was shut down for several hours Wednesday amid fears it would collapse.

The meteorological agency called on Niigata residents to be fully alert.

"We want people to brace themselves for tremors of lower six or even upper six" on the Japanese method of measuring earthquakes which goes up to seven, said Masahiro Yamamoto, who heads the agency's earthquakes division.

The initial quake of 6.8 on the Richter scale hit the Japanese reading of upper six, the intensity under which people cannot stand but have to crawl.

Nearly 2,530 people have been injured by the quakes since Saturday.

The earthquake was the deadliest to hit tremor-prone Japan since 1995, when 6,433 people were killed in the western city of Kobe.

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