The aircraft was found on Old Man Range, near Alexandra, by search and rescue volunteers.
Search teams in four-wheel drive cars and on motorcycles slogged through rugged central Otago terrain late last tonight in their search.
The aircraft was believed to be travelling between Bannockburn and Gore.
"We'd like to acknowledge and thank the tireless work of the Wakatipu and Central Otago Search and Rescue volunteers and Otago Helicopters staff who have worked throughout the night," police said.
Inquiries into the incident are ongoing and the Civil Aviation Authority has been advised.
A search and rescue spokesman this morning told RNZ that a rescue helicopter based in Queenstown joined the search on Wednesday afternoon, and the pilot reported thick cloud in the area of the crash.
After the chopper search finished for the night, ground crews using thermal imaging equipment and homing devices continued through the night until the body was found.
The spokesman could not give any information on the pilot, or nature of the flight.
- Additional reporting Otago Daily Times