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Gracie May McSorley died in July from severe head injuries, which police say were "inconsistent" with claims she had an accidental fall.
Michael Te Kouarehu Kereopa, 31, has now been charged with Gracie's murder.
An initial charge of assaulting a child was upgraded to murder in the Porirua District Court today, police said.
Following expert medical advice, police have alleged Gracie's injuries were similar to those that would be sustained in a high-speed car crash, and were deliberately caused by Kereopa.
He was in a brief relationship with Gracie's mother at the time of her death, police said.
Gracie was left alone with Kereopa on July 6 when her mother left to collect an older sibling, police said.
Gracie was described as "alert, happy and healthy" when her mother left, but 45 minutes later when she returned home, she was "very unwell".
An ambulance was called when Gracie became unresponsive, and her mother performed CPR on the baby until paramedics arrived.
The infant was then air-lifted to Wellington Hospital, and put on life support. However, she died the next day.
Her head injuries were "inconsistent with Kereopa's claims of an accidental fall", police said.
"Police are pleased that thorough investigative work has identified the defendant as the alleged offender in this case and he will now go before the Courts to be held accountable for his actions," police said in a statement today.
"However, this is yet another sad reminder of New Zealand's unacceptable levels of child abuse.
"We must all work together to keep our children safe and free from harm. Now a family is mourning the loss of a beautiful little girl at the hands of someone she should have been able to trust to care for her."