A Victoria Police spokeswoman said the human remains appeared to be that of a skull, but said the find still needed to be sent off for testing before it could be confirmed.
It is not yet known whether it belonged to a male or female.
Police and SES officers searched the shore and the shallows in the area this afternoon and cordoned off a crime scene.
It was also too early in the investigation to determine whether the grisly discovery was is linked to a missing persons case, police said.
“At approximately 11.30 this morning a fisherman has located partial human remains on the beach here at North Shore, police are now using the search and rescue crew and the SES just to search the area to see if we can locate anything else,” Detective Senior Constable Naomi Bourke said.
The homicide squad is not involved at this stage.
SES crews and divers from the police search and rescue unit will continue scouring the area until the sun sets.