The remains, which are yet to be identified, were found on Havelock Road in Clarkefield, northwest of Melbourne, about 3pm on Wednesday.
Police said the body was found by detectives probing a shooting at a Wildwood property, a short drive south of Clarkefield, about 7.20pm on August 19.
The victim, a 37-year-old man from Meadow Heights, is alleged to have been shot following a dispute with occupants of the property.
Police previously accused the alleged shooter, a 56-year-old Wildwood man, of placing the victim into a ute and driving off from the property.
He was captured on CCTV at two service stations in Greenvale during the early hours of the following morning before being detained about 5.30am.
He was charged with one count of intentionally cause serious injury after being interviewed by detectives.
But a sprawling search failed to turn up the 37-year-old victim, who was not visible in the CCTV footage.
An autopsy will be carried out to identify the human remains found on Wednesday, police said.
Detectives would consider alternate charges for the Wildwood man following the results of the autopsy, police said.
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