Investigators representing municipal forces and the RCMP began searching a parcel of land in rural Saanich on June 2 for the remains of Dana McKellar.
The 51-year-old was last seen in late August 2014, was reported missing by his family in September, and police say he was previously assaulted.
Victoria police say the coroners service will now try to confirm if the remains are human, and if they are, establish identity.
They say McKellar's family has been notified of the development.
Police also say businesses located at the search site have co-operated with officers, are not involved in the investigation and remain open for business.
At one point, police said more than 90 officers representing the Saanich and Victoria police departments as well as the RCMP were involved in searching a nearly three-hectare section of the property.
Officers used ground-penetrating radar, electromagnetic mapping technologies and aerial photography.
Police say investigators also consulted with experts in clandestine grave identification.