Authorities had been searching for the head of Mr Story, 39, since his dismembered body was discovered in the South Australian town of Port Lincoln on June 19.
On Thursday, a resident told police they had found a skull in scrub, Detective Superintendent Darren Fielke said.
"Preliminary investigations and phone calls to the forensic science centre have provided information that the remains are most likely human and I believe they are the remains of Julian Story," the Major Crime officer-in-charge said.
Former Beauty and the Geek reality TV contestant Tamika Sueann Rose Chesser, 34, has been charged with Mr Story's murder.
She was arrested on June 19 after Mr Story's body was found at the couple's home at Port Lincoln, on the Eyre Peninsula.
On June 27, Supt Fielke issued a plea for public help "because tragically, we have not recovered the head of Julian Story".
He said Major Crime officers had been redeployed to Port Lincoln following the discovery of the skull on Thursday.
"My understanding is that the person who contacted us today was walking their dog in that area," he said.
"The dog ran off into the scrub. The dog didn't come back when called.
"The person has gone in to see what's going on and that's how those remains were discovered."
Mr Story's family had been told of the discovery and "hopefully we can give them some comfort that we have found all the remains of Julian", Supt Fielke said.
"They are still planning for a funeral, which I believe will be towards the end of next week," he said.
The skull would be sent to Adelaide for forensic and scientific testing.
"If it's not Julian Story, then clearly we've got some other work to do, but I believe that it is," Supt Fielke said.
The murder scene was "suburbs away" from where the skull was found, in an area known as "slipway scrub".
Supt Fielke thanked the community for their help and said they had been through "quite a process" with the focus on their town.
A police guard had been placed on the site with more searches planned.
"If those are Julian's remains, Tamika is likely to have been in that location, so we don't know what other evidence may or may not be there," Supt Fielke said.
Chesser appeared in Port Lincoln Magistrates Court on Thursday via video link from James Nash House, a psychiatric facility in Adelaide.
She is also accused of assaulting a police officer the day after her arrest and faces unrelated charges of assault and disorderly behaviour.
The matters were adjourned and Chesser will reappear in court on December 18.
Detectives would be "guided by how her treatment is playing out", Supt Fielke said.
"We will speak to her at an appropriate time," he said.
In June, police released still images and video of a woman they allege was Chesser walking on Port Lincoln streets that were recorded after the killing, which investigators allege occurred about midnight on June 17.
The images show a woman wearing a black headscarf and black full-body coverings, carrying a bag.
Supt Fielke said police would not discount Mr Story's head was inside the bag.
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