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Emergency services were called to Frankton Station about 8.10am today and determined that a person was dead once they were at the scene, police initially said.
Police later confirmed to The New Zealand Herald that a dead baby was found alongside a woman's body on the tracks.
KiwiRail acting group chief executive David Gordon said a member of the public was struck by a freight train just after 8am.
"These types of events are deeply traumatic for those involved, and our thoughts are with all those affected," Gordon said.
"In line with our standard practice, our locomotive engineer has been put on leave and will be offered counselling and any other support needed from KiwiRail."
The line remains closed and there would be disruption to freight services between Hamilton and Tauranga.
An area had been cordoned off heading to Frankton Station.
Police are conducting a scene examination and offering support to those attending.
The deaths are expected to be referred to the coroner.