The incident unfolded in the tiny rural settlement of Balmoral, in Canterbury's Hurunui district, last night.
A Fire and Emergency NZ spokesperson said they received reports of the fallen tree just before 7.30pm.
St John ambulance staff treated the patient while they remained trapped.
Fire and Emergency shift manager Simon Lyford said the complicated rescue required heavy machinery and lasted hours, with a local contractor's digger and a farmer's tractor brought in to help.
Fire crews were able to remove the trunk of the tree and the person was freed just before 10pm.
It was not clear if the incident was caused by the weather, although there were severe thunderstorm warnings in the area earlier.
Efforts to get a rescue helicopter to scene were unsuccessful and it had to be stood down due to weather.
The person was instead taken to hospital by road. St John said the patient had critical injuries.
