George Gwaze was acquitted of the murder and sexual violation of Charlene Makaza at a High Court trial in Christchurch in May last year.
The Court of Appeal by a 2-1 majority in July this year overturned a bid by the Crown to have the Gwaze retried.
But now the Crown has applied to the Supreme Court for leave to hear an appeal against the Court of Appeal decision which a Crown Law Office spokeswoman told the New Zealand Herald was unprecedented.
Charlene, who lived with her extended family in Christchurch after being orphaned in Zimbabwe, was found unresponsive in her bed on January 6, 2007, and later died.
The Crown claimed Charlene died of suffocation after a sex attack in her bed in January 2008.
She was found by her aunt in bed having breathing difficulties and was rushed for medical treatment, but died in hospital some 18 hours later.
Medical evidence was given that damage to Charlene’s genital and rectal areas indicated she had been sexually assaulted. Sperm from Mr Gwaze was found on her underpants.
But defence counsel Jonathan Eaton said the death resulted from an infection that had overwhelmed Charlene, who had been HIV positive since birth.
Evidence suggested the sperm could have been the result of an "innocent transfer" in the family’s washing.
The appeal was based on "hearsay evidence" of South African paediatric surgeon Heinz Rode late in the trial.
He testified in a statement that Charlene’s symptoms were similar to those of Aids victims in South Africa.
Charlene had been HIV-positive since birth.
Two of the Appeal judges held that the Court of Appeal did not have jurisdiction to answer the Crown’s question of whether the trial should have been aborted.
On this basis the appeal was dismissed.
But the third member, Justice Grant Hammond, in a dissenting opinion, said he considered Gwaze’s acquittal should be set aside and a new trial ordered.
He considering that trial judge, Justice Lester Chisholm, erred in law by admitting into evidence Prof Rode’s hearsay statements and that improperly admitted evidence had a misleading effect and brought about a miscarriage of justice.
That consequence could have been avoided by Justice Chisholm aborting the trial, Justice Hammond said.