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.
“The crane operator was unharmed and has been arrested by police for questioning”.
Seven other people were injured in the accident.
“In the rush hour, this train would have been totally full”, he said.
According to Noten, the train was “travelling at speed” at the time of collision and the crane was moving over a “secure crossing”. Investigators were at the scene to establish the exact cause.
A spokesman said: “We can confirm that this morning at around 9am an Arriva train in the Netherlands has been involved in an accident near the town of Dalfsen”.
At the time of collision, which happened around 8:45am, it was reported that there were around ten to 15 people on board.
That accident happened in thick fog when a train driver missed a warning signal and the two trains hit head-on.
Train services along the line have been cut and the disruption could last several days.
“According to initial reports one person has been killed”, Mayor Han Noten told public broadcaster NOS, adding it could have been worse.