Charge sheets allege Mr Prestage and Ms Jeffrey murdered Ms Parfitt in Ballarat on April 28.
On Friday, a 35-year-old man, who is also at a correctional facility, was also charged with one court of murder.
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He will face Melbourne Magistrates Court at a later date, a police spokeswoman said.
Ms Parfitt, a mother of four, had lived at the Hickman Street home on and off for some time and was estranged from her family, whom she last saw in March.
In early December, Ms Parfittâs mother, Kathy Snowball, pleaded for anyone with information about her daughterâs disappearance to come forward.
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A second person has been charged with murder over the death of Ballarat mother Kobie Parfitt.
A 32-year-old woman who is currently in a correctional facility faces one count of murder, according to Victoria Police. She will appear at the Melbourne Magistrates Court on Monday.
Ballarat mother Kobie Parfitt.
Credit:Victoria Police
The fresh charge comes a month after Wendouree man Brendon James Prestage fronted court charged with one count of murder in relation to Ms Parfitt’s disappearance. The 31-year-old was arrested in Kinglake in December with the help of Victoria’s Critical Incident Response Team.
Remains police believe belong to Ms Parfitt were found at the bottom of a mineshaft last month at Snake Valley, a town 27 kilometres west of Ballarat. The 43-year-old vanished from her Hickman Street home in Ballarat on April 28.
A man arrested over the death of Ballarat woman Kobie Parfitt has fronted court after being charged with her murder more than six months after the mother of four vanished from her home.