It's understood this man was a former partner of Ms Fraser.  The Paynesville man has been questioned by police in relation to her death but released without charge.

Police are also investigating whether the crime scene was tampered with.

Two pairs of gumboots were all that remained at the front door of the modern grey home on Friday afternoon. Two children’s bikes also rested alongside the house.

The property is nestled among trees and partly obscured from view.

Alice Bradley, a friend and colleague at Cowes Medical Centre, said Ms Fraser had shared fears about her safety  and that of her children in the months leading up to her death.

Her parents had also moved into the home recently and it is believed they were also concerned about her safety, but they were overseas at the time of her death.

"She had mentioned to me a lot that she felt unsafe ... at times she was really frightened," Ms Bradley said.

She said that Ms Fraser had worked at the Cowes Medical Centre a couple of days a week for two years, treating both adults and children as a psychologist.

"She was a great mum, she was very involved in the local school, she had a large group of friends," Ms Bradley said.

"She was very popular and just gorgeous."

Ms Fraser dropped off her two daughters and son in the morning, then caught up with friends for coffee between 9am and 11am. She told them she had a midday appointment, but she did not show up.

Police visited her home at 4.30pm to check on her due to concern for her welfare, and they found her body in the garage.

A post-mortem was conducted, and homicide squad detectives have taken over the investigation.

"Based on the circumstances of her death, it is strongly believed to be suspicious and will now be investigated by detectives from the homicide squad," a police spokesman said.

Detective Sergeant Sheahan did not specify the cause of death but said Ms Fraser suffered "assault injuries".

"I can't confirm to you if it's random or targeted, but as I said, I don't have a concern for the safety of the community here. There are extra police resources dedicated to the area and investigating Samantha's death," he said.

Peter Fusinato, the local area commander for Bass Coast, said the death had hit the community particularly hard.

"There is a sense of loss. Samantha was well known, she had three young children at the primary school ... naturally [the community] is grieving," he said.

One of Ms Fraser's neighbours, Sue, said Ms Fraser lived at the home with her children and her parents, but her parents had been overseas on holiday when Ms Fraser died.

"We are devastated. It's horrible. It's just so sad, she was so young and with a young family and we feel for the kids," Sue said.

She said Ms Fraser had lived at the property for the past four years.

The last time Sue saw Ms Fraser, who was known locally as Sam, was on Sunday when they waved at each other from the front garden.

She said Sunday had been Ms Fraser's birthday.

Another neighbour confirmed Ms Fraser's parents had been in the US for a holiday when the incident occurred, but had since returned to care for the three children.

"It's so sad, she was beautiful. Just a beautiful girl," she said.

She said Ms Fraser was once married, but had split from her partner.

Another colleague, Dr Adam Wilson, said they were struggling with the news.

"I know she was loved by our reception staff, nurses, doctors, so a lot of people in our work environment are struggling," he told radio station 3AW.

"People are just very shocked about what happened."

A fundraiser has been started for Ms Fraser's children, with donations already topping $20,000.

Detectives are appealing to anyone with dash cam footage from Philip Island, particularly between Seagrove Way and San Remo, as well as CCTV footage near the property where Ms Fraser was found.

They also wish to speak to anyone who may have entered the Seagrove Way property on the day of Ms Fraser's death, or anyone who noticed suspicious activity around her property over the previous days.

Police would like to speak to anyone who can provide information on Ms Fraser's movements between 11am and 3.30pm last Monday.