John Torney, 40, faced Shepparton Magistrates Court on Tuesday via video link from prison over Emma Bates's death earlier this year.
The 49-year-old was found dead inside a Cobram property, near the NSW border, on April 23.
Police alleged the pair knew each other, and initially charged Torney with 13 offences including intentionally causing injury, several counts of assault and breaching a court order.Â
However, prosecutor Alex Turner on Tuesday said an additional and more serious charge of negligent manslaughter had been laid against Torney on Friday.
"The determination to lay the charge that brings the matter to the indictable jurisdiction was off the back of a report completed by the Victorian Institute of Forensic Medicine," he told the court.
Torney's defence lawyer asked for prosecutors to pay legal costs for three previous court dates due to delays and changes to charges.
"Had this charge been laid earlier and medical material considered, there would have been no utility in those appearances," Kyle McLaughlin said.
"Those costs have ultimately been thrown away."
Mr Turner apologised for some of the delays in his communication with defence as he said he was on unexpected sick leave including a stint in hospital.
However, he objected to the state paying costs for two of the dates, including one which was Torney's bail application.
Magistrate Allison Vaughan approved the cost application for two dates, and ordered the chief commissioner of police pay Torney's defence $780.
Torney was remanded in custody and will next face court in March 2025.
In 2016, Torney was acquitted of murdering a toddler after the two-year-old girl's beaten body was discovered in the roof cavity of a Mildura house.
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