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A Fire and Emergency New Zealand (Fenz) spokeswoman said it was called to the Alliance Group Pukeuri Plant just after 3.15pm today.
Fenz were assisted at the scene while waiting for a helicopter to arrive to pick up the injured person.
The train was at the plant and not on the main line between Dunedin and Christchurch.
A St John spokesman said a seriously injured man was airlifted to Dunedin Hospital.
An Alliance Group spokesperson said it had launched an internal inquiry into the incident.
''Alliance will be supporting the employee’s family and speaking with WorkSafe New Zealand.
''It would be inappropriate to comment further at this stage.''
It confirmed the incident involved an employee.
An Otago Daily Times reporter at the scene said three police cars, two fire appliances and St John were in attendance.
A helicopter landed at the site about 4pm and left about 4.30pm.
Alliance Pukeuri staff members at the scene declined to comment.