"KiwiRail's thoughts are with everybody involved," she said.
Trains are returning to schedule after the incident.
Police said the serious crash unit has been called in to investigate, and surveillance cameras will be reviewed.
The man today is not the first wheelchair user to be hit by a train.
In 2013, a woman's wheelchair became struck at a crossing in Auckland. Two passersby rushed to help as a freight train approached but could not free the trapped chair and instead tipped it roughly.
The woman suffered horrific injuries as the train hit the edge of the chair, dragging her along the track until the driver could stop.
Also that year in Wellington, a wheelchair user was dragged for 1.7m while a mobility hoist was in operation to help her and her companion leave the train.
Nobody was injured.