A homicide investigation was launched in April following the death of a 52-year-old woman at a Lemnos Ave property in Karori.
Police were alerted to the incident at around 1.10pm on April 5, and found the woman's body on arrival.
A seriously injured 12-year-old girl was found in the same bedroom as the woman's body.
Borton, 30, also faces charges of sexually violating the girl twice and indecently assaulting the woman by removing her underwear.
He is also accused of entering a Lemnos Ave property on the day of the alleged killing with a steel mallet, with intent to commit an imprisonable offence.
His other charges are two counts of entering a building with intent to commit an imprisonable offence between February 9 and April 5, doing an indecent act on the girl, impeding her breathing by blocking her nose and mouth - and wounding the child with the intent to cause grievous bodily harm.
The child has automatic name suppression due to her age and the sexual nature of the charges, and the dead woman has interim name suppression.
Police have said they are not seeking anyone else in relation to the incident.
Borton is alleged to have killed the victim between April 4 and 5.
