Police probing the alleged 2011 slaying of Nicholas Katopodis found the remains under a house on Gladstone Avenue at Mount St Thomas, on Saturday afternoon.
The remains will be taken for a examination to formally identify them and to establish a cause of death, a police statement says.
In September 2011, a 40-year-old man from Mount St Thomas was charged with murdering Mr Katopodis, despite no body being found.
The man is in custody and is assisting police with their inquiries, with the matter before the courts.
Police have previously alleged that Mr Katopodis was murdered after a night out at a Figtree pub with friends.
Source: Sky News Australia