An address in Taupo has been contained overnight for a scene examination today.
"It is very early into the investigation and I am not prepared to speculate on how the boy died," Mr Warner said.
"We have a number of people we need to speak to and the investigation will also rely heavily on information and advice from medical experts; so it may be some days before we are in a position to make more informed comment."
He said police will not be commenting on the nature of the injuries.
Other children from the address have been taken in to CYF care pending the outcome of the investigation.
The name of the boy will not be released until all relevant next of kin have been informed.
An email was sent to Taupo District Councillors this morning advising them of the investigation.
They were told a "homicide" investigation was underway following the death of a 3-year-old boy.
Child, Youth and Family Central Region Director Sue Critchley said: "We are focusing our efforts on working with the family to ensure the safety of all the children in the household."
Housing New Zealand confirmed the address that has been cordoned off belongs to the organisation.
