Victoria Police say the light aircraft was discovered in dense bushland 30km east of Tallangatta shortly after 10am on Monday.
The man's family has been contacted and police believe he was the only person aboard the aircraft.
Senior Sergent Shane Martin told reporters in Tallangatta that police would work with the Australian Transport Safety Bureau to determine the circumstances of the crash.
Sgt Martin could not confirm when the body would be extracted from the crash site.
"It's very dense here. It's a mountainous terrain, very dense where it's been located. " he said.
Sgt Martin said the investigation was ongoing, and it was unclear whether the wreckage could be extracted.
"That's part of the recovery phase in relation to trying to work out how we can recover the plane," he said.
"Obviously, our first operation is to recover the person on board the plane."
The Australian Maritime Safety Authority led an extensive search between Mount Beauty and Corryong, following reports the pilot had failed to reach his destination on Sunday.
Sgt Martin said it was understood the plane took off from Mount Beauty Airport and was destined for Wollongong.
An AMSA spokesperson said the aircraft was reported overdue at just after 2pm on Sunday.
"About 10am on Monday, after a search of the area involving multiple aircraft and ground crews, a Victorian Police helicopter located the crash site about 30km east of Tallangatta in the northeast Victorian high country," the spokesperson said.
"Victoria Police have confirmed the pilot of the aircraft was found deceased at the scene.
"AMSA acknowledges this is a difficult time for family and friends of the pilot and would like to thank all those who assisted with the search."
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