Marat Ganiev, 55, had been accused of killing Isla Bell in the early hours of October 7, 2024, before hiding her body in a fridge.
Her remains were found at a rubbish tip in Melbourne's southeast six weeks later.
Ganiev was originally charged with murder but that was downgraded to manslaughter as the case entered the Victorian Supreme Court.
Crown prosecutor Jeremy McWilliams on Tuesday told the court the manslaughter charge against Ganiev had also been withdrawn.
Ganiev will instead be charged with attempting to pervert the course of justice, with a fresh indictment expected to be filed later on Tuesday.
A new trial date is yet to be set but a summary of the allegations will be served to the defence within the next fortnight.
Ms Bell's grandfather David Spokes said it was a very difficult day for his family.
"There are many things that I would like to say but I can't say today because there are more charges pending," he told reporters outside court.
"We have done our utmost not to jeopardise that. At the appropriate time, we will have more to say."
Ms Bell's mother Justine Spokes also expressed her disappointment.
"I raised Isla to be full of compassion and care and integrity and strength," she told reporters.
"We're just living in a society with hearts of stone."
Eyal Yaffe, 59, was also originally accused of assisting an offender and attempting to pervert the course of justice in relation to Ms Bell's death.
Mr McWilliams on Tuesday also confirmed Yaffe's charges would be discontinued.
Yaffe declined to comment as he used crutches to walk out of court a free man.
A spokeswoman for the Office of Public Prosecutions confirmed the charges had been withdrawn due to "insufficient evidence" to support the offences.
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