Detectives made the discovery while executing a warrant at a house in Fongeo Drive overnight.

They are yet to identify the remains and continue to investigate a number of leads.

Ms Cafferkey, 22, was last seen by her family more on November 9. She has not accessed her bank account since.

Homicide detectives took over the investigation after it emerged that she had received threats from a male friend in the lead-up to her disappearance.

"Due to the length of time that she's been missing and that her car was found in a location that her family is not familiar with, the investigation is now being conducted by the homicide squad," a police spokeswoman said on Saturday.

Friends of Ms Cafferkey said on Facebook that a male friend had posted threatening messages to her in the days before she disappeared. The messages have been shown to police and are no longer on her Facebook page.

Ms Cafferkey's 2001 Astra sedan was found in Owen Street, Maribyrnong, on Thursday night. At the time, police said there was no evidence of foul play. But investigators remain concerned for her welfare and are pursuing "several lines of inquiry", a spokeswoman said.

Police have said that Ms Cafferkey needs regular medication for a rare asthma-related illness.

Jennifer Wojcicki posted on Ms Cafferkey's Facebook page on Saturday: "I've lost [hours] of sleep over the week. I've been so stressed and scared, my brain is in over drive thinking, I've cried so many tears, I've watched and read more news segments than ever before in my life, and I've never felt more helpless, all this because I care and love you.

"The girl I've known since the day I was born. The girl I know with the gorgeous smile and the bubbly infectious personality. Please be ok safe and well and home with your family and friends soon."

Catt Angwin posted to Ms Cafferkey on Friday: "I cant stop thinking about your gorjus [sic] smile that always lights the room up .. I just wanna hear you safe and okay! love you sarBear. "

Anyone with information is urged to call Crime Stoppers 1800 333 000.

- with Maris Beck