Police arrived at the property around 3.30pm to help the family in extending the search for the toddler.
"It was then that a neighbour and the father made the discovery," he said.
"It looks like the toddler has walked away from the property and wandered in to the river."
He said the death was not being treated as suspicious and the coroner had been informed.
Mr van der Wetering said the boy's family were distraught and they were being helped by Victim Support.
He said the river was 200 metres from the family's property.
"Our deepest sympathy goes out to the family because of this tragedy," Mr van de Wetering said.
UPDATED 11.13am: Police have confirmed the missing Waihi toddler has been found dead.
Police said 3-year-old Ezra Tapp appeared to have drowned in the Ohinemuri river at Waihi about 3pm yesterday.
Police were first called to the address when family members discovered the boy missing. Shortly after that his body was found.
"Our deepest sympathy goes out to the family because of this tragedy," Hamilton Senior Sergeant Pete van de Wetering said.
UPDATED 8.19am: Police are yet to respond to reports that a child has died after going missing in Waihi yesterday.
The 3-year-old was reported missing at 3pm.
This morning Waihi police Senior Sergeant Aaron Fraser said police would be issuing a press release later this morning about the missing child but would not comment further.
EARLIER: A three-year-old was reported missing from Waihi at 3pm today.
Inspector Brooker of police northern communications said police received a call about a missing three-year-old from Waihi at 3pm.
Waihi police declined to comment.
