Under floodlights, rescue teams combed wrecked carriages all night for casualties, also using torches on their mobile phones.
The crash also injured 84 people, the ministry said in a statement.
The Twilight Express Mizukaze departed Osaka on its maiden trip with around 30 well-heeled passengers on a journey to the far reaches of Japan's main island.
The driver is among those injured and is in critical condition at the hospital, the company added.
At least three people have been injured and others trapped after a train travelling to Switzerland derailed
The train will run daily with a journey time of around nine and a half hours, Turkish State Railways official says
The passenger service from Thionville in northeast France hit the goods train near Bettembourg close to the French border around 0800 GMT, they said.
The 750 kilometre (460 mile) railway, built by two Chinese companies, will link Addis Ababa to the Red Sea port city of Djibouti in about 10 hours, a far cry from the current excruciating multi-day trip along a congested, pot-holed road.
The train stopped in the northern village of Osorno at 9:15pm on Tuesday, two hours after it left Santander for Madrid because the driver said he had "exceeded the hours of his shift", state-run operator Renfe said in a statement.
More than 20 wounded in Manisa, when train crashes into minibus carrying farm workers in the early morning
The Mayor of Dalfsen in Netherlands has told Dutch radio that 2 people have died in a train accident.
Despite no trains currently travelling to western Europe, thousands of refugees have stormed a train to safeguard their way out of Hungary.
France's national rail company SNCF said it had ordered 2,000 trains for an expanded regional network that are too wide for many station platforms, entailing costly repairs.