Because of the lack of daylight, firefighters left the scene and returned about 7am to clean up the railway.
Williams said fire crews would be going through a debrief to make sure all firefighters who attended the incident were taken care of.
A police media spokeswoman said a formal identification process was under way and police were investigating the incident.
A police officer, two KiwiRail staff and a local kaumatua could be seen at the railway track about 8am yesterday. The kaumatua had blessed the area.
Residents in the area said the tracks were regularly used by people walking home from Te Puke at night.
A KiwiRail spokesman said the freight train had been travelling from Mount Maunganui to Kawerau when it struck a person on the tracks.
"Following standard procedure, the driver has been stood down and is being offered counselling," the spokesman said.
The latest fatality involving a train follows the death of two other men since the end of February.
On April 3, a 38-year-old Whakamarama man was found dead on top of a train at the Port of Tauranga. Police said the man appeared to have fallen from an overbridge in the Whakamarama area and landed on top of a train carriage.
On February 23, a man died after a collision between a farm vehicle and a train near Apata Station Rd.
Rail safety group TrackSAFE said there had been five deaths throughout the country to date in 2018, with three of them occurring in the Bay of Plenty. Last year, there were 16 deaths nationwide on our rail network.
TrackSAFE foundation manager Megan Drayton said the organisation planned to continue to work with local councils, KiwiRail and police on raising awareness of the safety issues around the rail network and to educate people on how they can stay safe when crossing tracks.
"Our thoughts are with all those in the Bay of Plenty affected by these incidents, including our locomotive engineers (train drivers). These events are particularly traumatic for them," Drayton said.