Photos of the crash in Dalfsen, 120 km (75 miles) east of Amsterdam, showed four passenger cars on their side after colliding with the crane.
Mayor Han Noten told Dutch radio broadcaster NOS that one person had died in the crash. The train was operated by Arriva, a subsidiary of Germany's Deutsche Bahn.
A spokesman for Arriva could not immediately be reached for comment.
"There were not too many people on the train. The evening train is usually full, but not in the mornings."
Local police told AFP only that a train accident had occurred but would give no further details.
An eyewitness told NOS that the crane was on caterpillar tracks and was moving very slowly as it crossed the railway line when the train arrived.