Emergency services were called to the site of the crash in Waimarino Forest, near Raetihi, Ruapehu, shortly after this morning's accident.
Due to the remoteness of the area, fire, ambulance and police, took more than 40 minutes to reach the wreckage and the pilot.
Palmerston North rescue operator Lance Burns said the chopper couldn't land and the 29-year-old man had to be winched out.
"It was steep terrain and a lot of gorse bush, but we got him out as safely and quickly as we could."
He said it took the Palmerston North Rescue Helicopter about 22 minutes to get to where the man had crashed.
A rescue hoist was used to drop the onboard paramedic down to the injured man who was stabilised on site.
Once stable, together with the St John paramedic, the pilot was hoisted back up to the waiting helicopter, before being airlifted to Whanganui Hospital a little after midday.
The rescue chopper landed at the hospital at 12:45 and the injured pilot was transferred to its emergency department.
A Whanganui hospital spokesman said later in the afternoon the man was in a serious but stable condition.
Earlier today Rescue Coordination Centre New Zealand spokeswoman Tania Shingleton said the rescue helicopter had flown in from Palmerston North to the crash site.
"The pilot is conscious and breathing," she said.
St John's spokesman Mark Tregoweth confirmed ambulance staff had treated the pilot at the scene, before he was airlifted to Whanganui Hospital with serious injuries.
Police said in a statement the pilot was the only person on board. Staff are currently supporting his family.
An investigation into the cause of the crash would be handled by the Transport Accident Investigation Commission.
