A man – believed to be the last one inside – was found dead early on Monday, a Yamagata prefectural police spokesman said on condition of anonymity.
Another man and two women, aged 22 and 51, had been found dead earlier, the spokesman said.
Five cars of the six-car express train derailed on Sunday evening, and three of the cars toppled onto their sides in Yamagata.
Rescuers crawling through wrecked carriages during a severe snowstorm had found the bodies of the four passengers.
The injuries of the survivors outside the wreckage did not appear to be life-threatening, but it was not known whether those trapped inside were still alive, Yoshikatsu Oe, another Yamagata police spokesman, said.
The train derailed in strong winds soon after it crossed a bridge over a river, police said. It was travelling between Amarume and Sakata stations on the Uetsu line, 350km north of Tokyo when it derailed.
The train operator reported that the train driver, who survived the crash, had applied the brakes manually after hearing an unusual sound.
About 107 people were killed and nearly 550 injured when a commuter train jumped the tracks and smashed into an apartment tower in the western city of Amagasaki in April, in Japan’s worst rail accident since 1963.