Sio appeared in Rotorua District Court on Monday. He was remanded in custody and is due to reappear on March 3.
Police said further charges were likely.
A Lakes District Health Board spokeswoman said the organisation would not provide any information because the matter was being handled by police.
Neighbours earlier told the Rotorua Daily Post they woke up on Sunday to find a Union St home cordoned off.
Resident Craig Nelson said he saw "police everywhere" down the street on the weekend.
"It's sad to hear that the baby [child] died."
He said the parents of the child were new to the neighbourhood.
He had only seen the 5-year-old once but there was nothing unusual and he was "just playing like a normal child".
"I don't know what happened ... This is a beautiful neighbourhood, nothing really goes on around here. Mainly tourism - hotels down the road."
A woman who lived next door to the property, who only wanted to be known by her first name, Vaishali, said she woke up early on Sunday to see police had sealed off the house and there were three police cars outside.
Police later visited her home and asked if she witnessed anything.
They said the circumstances were "all confidential" while police interviews and forensic examinations took place.
She said she had seen both a young boy and a young girl at the home on various occasions.
A child's blue and black tee shirt has been placed on a tree near the property.
A flax flower wrapped in a blue a ribbon has also been placed on the tree in the boy's memory, with "rest eazy neff" written on it.
