The line was closed for about four hours while police investigated but has reopened.
In a separate incident, St John ambulance treated another male for minor injuries who was then taken to Te Kuiti Hospital but the Herald understands he was not with the victim when he was hit by the train.
A police spokeswoman confirmed that just one person, a teenage boy, was hit by the train.
Another male was taken to hospital and treated for minor injuries as a result of an unrelated incident, she said.
Mr Miller said KiwiRail would be conducting its own investigation into what happened and reminded people to be careful when near rail lines.
"Our thoughts are with the families involved."
In a statement, police said they were providing support to the young boy's family and the train driver.
The incident had been referred to the coroner, police said.
Police had completed initial inquiries and had referred the incident to the coroner.
Police said no further information regarding the circumstances of the incident or details of victim would be released as the matter was now before the coroner.