"It's quite a rural area. The car's appeared in front of the train driver who made every effort to stop but unfortunately it's hit the vehicle side-on in the middle of the car.
"Initial thoughts are that the guy hasn't realised that there's a crossing there and happened to go over the crossing at the same time as the train was coming.''
An ambulance spokesman said the driver of the car was treated at the scene before being flown to Wellington Hospital in a critical condition.
The section of State Highway 1 was closed for about 40 minutes to allow the rescue helicopter to land at the scene, but has since reopened.
A New Zealand Transport Agency spokesman said traffic had been delayed by 10 to 15 minutes while a detour was in place.
A KiwiRail spokeswoman said the train was carrying freight from Wellington to Auckland.
There was a stop sign where private road intersected the railway but not barriers or alarms.
"Barriers and alarms are at the more major crossings around the country,'' the spokeswoman said.
The train driver would be stood down and offered counselling.
KiwiRail would conduct its own investigation along with the police's inquiries.