The train hit a hydraulic crane on a crossing, tilted over and went into a field, leaving several carriages lying on their sides.
According to residents, the crane had been crossing the line, east of the city of Zwolle, when the train ran into it.
The local mayor said one person was dead. Another six were hurt, and one had serious injuries.
Witnesses said the train driver had been killed but there was no immediate confirmation from the operator, Arriva.
Mayor Han Noten told Dutch media that 10 to 15 people had been on board at the time of the crash, shortly before 09:00 local time.
“Luckily it wasn’t the busiest train, so as regards casualties it won’t be as bad as it could have been,” he said, although it was a tragedy for the dead and wounded.
Emergency services said some managed to clamber out of the carriages but they were searching the wreckage for anyone still trapped.
The train had been heading east from Zwolle, RTV Oost reported. Local services on the line were likely to be disrupted for the rest of the day while an investigation was carried out by the Dutch Safety Board.
Police were talking to the crane driver who had managed to jump clear shortly before the accident.
It was not yet clear whether he was being treated as a suspect. Little was left of the crane’s cabin after the crash.
There were 30 accidents on Dutch level crossings in 2015 which claimed the lives of 13 people, reports said.
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