A body - likely to be missing helicopter pilot Matthew Wallis - has been found in Lake Wanaka, capping off a three-day search.

Police said about 10pm tonight they found and recovered a body, believed to be Matthew Timothy Wallis, from the Stevenson's Arm area of Lake Wanaka.

Helicopter pilot Matthew Wallis. Photo / Supplied
Helicopter pilot Matthew Wallis. Photo / Supplied

He had been missing since Saturday afternoon after what was meant to be a short 15-minute flight.

The Police National Dive Squad and the Navy retrieved the body and some wreckage of a helicopter.

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"This is the best possible outcome we could have hoped for in the circumstances", Detective Sergeant Derek Shaw said.

"We are glad to be able to bring some degree of closure to Matthew's family at this sad time.

"Police would like to thank the Wallis family, New Zealand Defence Force, LandSAR volunteers, the Wanaka community and the aviation industry for their assistance in this recovery operation.

"Matthew's family ask the media to please respect their privacy as they come to terms with their loss."

Now the matter will be referred to the Coroner and the Transport Accident Investigation Commission (TAIC) is investigating.