A man believed to be the last one inside was found dead early Monday, a Yamagata prefectural police spokesman said on condition of anonymity, citing departmental policy.
Five cars of the six-car express train derailed Sunday evening, and three of the cars toppled onto their sides in Yamagata prefecture, about 180 miles north of Tokyo.
The injuries of the survivors taken to hospitals did not appear to be life-threatening, said another Yamagata police spokesman, Yoshikatsu Oe. Most of the injured passengers were riding in the first two cars.
Rescuers plan to lift the wreckage to see if any survivors are beneath it. It was unclear how many passengers were on the train; one official had earlier said it was 30, but the tally of the injured and trapped indicated it was more.
The police spokesman said all passengers died in the first car, which smashed into a nearby pig pen and buckled in the middle.
Transport Ministry official Ryotaro Miyamoto said four accident investigators headed to the site Monday, and more experts were to be dispatched later in the day.
Railway operator JR East Co. President Mutsutake Otsuka apologized for the accident at a news conference early Monday and promised a thorough investigation.
"We apologize for causing the extremely serious accident," he said. "To fulfill our responsibility as a railway operator, we'll fully investigate the cause of the accident and prevent a recurrence."
Another Transport Ministry official Hiromi Mishima said the cause of the accident was not immediately known, and officials are still trying to assess the damage.
Yamagata police official Yasuhiro Sugiu, however, said there had been high-speed wind warnings for the area. Public broadcaster NHK quoted the train conductor as saying a strong wind hit the train just before the accident, and Kyodo News agency reported winds of nearly 48 miles an hour were registered near the site of the crash.
Japan in recent days has suffered from unusually heavy snowfall and blizzards have lead to the deaths of eight people, but snow did not appear to be a factor in Sunday's crash.
NHK footage of the wreckage site showed the train derailed in a rural area, but there were only patches of snow on the ground.
The train was en route from northern Akita prefecture to Niigata prefecture when it went off the tracks at about 7:20 p.m. (1020 GMT).
A train derailment on April 25 in Amagasaki, western Japan, killed 107 people and injured more than 500 others. It was Japan's worst train wreck since 1963.