The 10-month-old boy, Mustafa Ali, was brought unconscious to Te Kūiti Hospital on Saturday afternoon.
"Tragically, despite the best efforts of medical personnel, he was unable to be resuscitated," detective inspector Graham Pitkethley said. Police have launched a homicide inquiry.
Mustafa's injuries were the result of violent blunt force trauma and did not appear to be accidental. A post-mortem was expected to take multiple days, he said.
At this stage police believed both Mustafa's mother and father took him to the hospital and the fatal injuries took place the same day.
They have both spoken to police but Pitkethley said he had concerns there were inconsistencies with their statements.
Mustafa's father has denied any wrongdoing.
"Mustafa Ali is known to police in regards to a non-accidental injury previously that has been investigated," Pitkethley said.
Police were notified of this incident in October and Pitkethley said the investigation has been ongoing since.
At the time Mustafa received fatal injuries police believed his mother, family and potentially two other people lived at the house.
Pitkethley was asking for anyone in the community with information to come forward, including anyone who heard screams coming from the house.
Non-accidentally injuries on children were one of the most complex cases police could work on and complexities were present in this case too, he said.
Police will continue to speak to family members.
Oranga Tamariki said it was was notified of Mustafa's death.
The death was "a huge shock to the community", Waitomo District mayor John Robertson told Morning Report.
"We have our tragedies from time to time, but no community wants to see a 10-month-old baby apparently suffer like this baby did."
Te Kūiti had a population of 4500 people, he said.
"A lot of sympathy goes to those who knew the child but shock at the fact that this could happen in our community."
