Police say Ms Gilligan is the only outstanding missing person known to have been in that area in recent years, but it will take at least a month before the skull’s identity is determined.

Ms Gilligan was last seen putting fuel into her car in Avoca on March 26, 2010 – the day after her family reported her disappearance.

Later that night her red 1993 Holden Barina sedan was found abandoned in Wycheproof.

The skull was found by a fox hunter, on the banks of the Avoca River near Charlton on Saturday.

A police search for the rest of the skeleton is planned for next week.

Ms Gilligan’s children Tanya and Kerrie Patmore and Gavin Yates were sombre about the finding, but said it would provide some solace if the skull turned out to belong to their mother.

“That’s the worst part, not knowing I think,” Tanya said yesterday. “Since we got the phone call I’ve been having nightmares. In one way it would be a relief (if it was her) because then we could put her to rest properly.”

Kerrie said the family had struggled to deal with the lack of information.

“In the last year we haven’t really heard nothing off the police and then out of the blue we got that,” she said. “It was only lucky that there was a guy out shooting foxes and he happened to see the skull sitting in the water.”

Detective Senior Constable Steve Campbell said all of Ms Gilligan’s family members had been advised of the finding. “It’s been quite perplexing. Normally there’s a reason why a person would disappear and why a person would end up at a particular place,” he said.

Anyone with information about Ms Gilligan’s disappearance should call Ballarat police on 5336 6080 or Crime Stoppers 1800 333 000.