"Police dispatched to the scene found the crashed helicopter in a dense spruce forest and inside it the body of the owner and pilot of the aircraft, Peedu Ventsel," Aivar Otsalt, chief of the South Estonian police told the Baltic News Service.
Police cordoned off the area, and experts who must establish the cause of the accident were due to arrive shortly.
The helicopter had suffered extensive damage and apparently had caught fire after the crash.
The regional police chief added that the crash site was within the area designated for the search and that even if the local resident hadn't found the wreckage, searchers would have come across it soon.
Ventsel and his Robinson R-44 four-seater went missing near the Vortsjarv lake on the evening of May 11 as the amateur pilot was returning from Tallinn.
The helicopter, owned by Ventsel and run by the Pakker Avio company, was last heard from at 10:46 p.m. when it was flying near Vortsjarv's eastern shore in the Kurekula region, spokespeople for the Border Guard Board have said.