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Lister Helicopters confirmed one of its machines, a Eurocopter Squirrel AS350, was involved in the crash at Deep Creek, west of Dunedin.
A police spokeswoman said police were alerted at 5.30am that a helicopter flying from Milton to Alexandra was overdue.
The aircraft is believed to have flown over State Highway8, towards Lawrence, over Glendhu Forest.
A Rescue Co-ordination Centre New Zealand spokeswoman said the crashed helicopter was located about 7.30am by a search helicopter sent from Dunedin.
The sole occupant had not survived, she said.
Lister Helicopters owner Alister Lister said the company was "devastated" by the accident.
"We have lost a much-loved employee and friend.
"Our thoughts are with the family at this dreadful time.
"Lister Helicopters is now working with all of the agencies involved in investigating this tragedy."
Mr Lister said no further comments would be made until the investigations were complete.
The Transport Accident Investigation Commission (TAIC) has launched an inquiry into the crash.
It was appealing for any witnesses who heard or saw the aircraft or had captured it on photo or video, a spokesman said.
The crash site was at the south end of the Lammerlaw Range at an elevation of 800m.
The commission had appointed an investigation team of three, which anticipated reaching the accident site this morning.
TAIC had issued a protection order prohibiting unauthorised access within a 200m radius of the main wreckage and any unauthorised handling of any other wreckage or evidence.
It would be investigating the background of the helicopter pilot and of operational staff.
It would also be considering the history, performance and maintenance of the helicopter itself and the operating environment.
Lister Helicopters was formed by Alister and Nadine Lister in June 2011.
Its website says it operates four helicopters from its South Otago base, and provides agricultural, commercial and scenic flight services.
— Additional reporting Richard Davison and The New Zealand Herald