Trustpower TECT Rescue Helicopter pilot Liam Brettkelly said the 60-year-old local farmer sustained multiple injuries, including serious leg and head injuries in the crash.
The initial caller phoned St John at 3.29pm.
KiwiRail said the train was travelling between Mt Maunganui and Kawerau when the crash happened.
"The collision took place on a private, unsealed level crossing. Some delays to freight services are expected," a spokesman said.
"The locomotive driver was uninjured. In line with normal practice, he has been relieved.
No other information is available at this stage."
Pukehina local Ash Hiltonn said the crash happened on the driveway of a rural property which was intersected by the train tracks.
The 21-year-old saw a chopper circling overhead and emergency services vehicles attempting to free the bike from under the train.
"There were two fire trucks, the helicopter had landed, and there were about six police cars and two ambulances," she said.
Fire trucks appeared to be trying to lift the train car off the tracks to free the vehicle.
Hiltonn said the crash had happened on a driveway of an orchard off the main road.
She said there were five to six freight cars past the point of the crash, suggesting the man had hit the side of the train as it was moving.
"It was really weird because it seems like the train was quite a lot further up - it wasn't like they tried to cross before the train got there."
