The 34-year-old was arrested at the property in Port Lincoln, on South Australia's Eyre Peninsula, on Thursday after police and emergency services were called to the home.
Specialist detectives and forensic officers flew to the scene on Thursday night and are helping local police, with the investigation described as complex.
The woman appeared in Adelaide Magistrates Court on Friday via phone link from Port Pirie Hospital.
She is also charged with disposing of human remains to pervert the course of justice and assaulting a police officer.
The woman is being held under a mental health detention order and the court imposed a suppression order on her identity.
SA Police Assistant Commissioner Ian Parrott said there "were a lot of unanswered questions" in the investigation.
He confirmed the woman and man were in a relationship and both lived at the property.
"There's a number of inquiries to be made and there's a number of things that we still don't know," he said.
"It is such a complex scene that we have got there, so it will take some time to understand the exact nature of what's occurred."
Mr Parrott said forensic specialists were working to determine the man's exact cause of death.
The woman will return to court in December.
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