Police were called to an address in the suburb of Bader about 5.20pm on Sunday afternoon, after reports of a violent altercation.
Three people were taken to hospital - the boy, and two adults who were moderately and seriously injured.
The child died on Sunday night in hospital.
Hamilton City field crime manager Inspector Darrell Harpur said the man was taken into custody at the scene and police had launched a homicide investigation.
"Police are not seeking anyone else in relation to what happened, however will remain in the area as they continue a scene examination and further inquiries."
At the house at the end of a quiet cul-de-sac, washing could be seen hanging on the line in the back yard. A child's bike, barbecue and an old fridge were among items strewn in the front yard.
Neighbours said loud music and parties could often be heard coming from the house, with a man doing renovation work nearby saying he had been warned the house was used by a gang.
Another neighbour said she knew the family but would not comment, saying the family had requested she not say anything.
A furniture removal truck also sat in the driveway of the home.
The man accused was due to appear in court on Monday.
A relative of the boy paid tribute to him on social media on Monday afternoon. The woman said whānau were waiting to take the boy's body home to Whakatāne.
She said his father, who was understood to have been one of the two adults injured during the altercation, was stable in hospital and awaiting surgery this afternoon.
It appeared the boy's mother had died at an earlier time.
"Rest in the arms of mum our boy... Rest in eternal love MyBro," she wrote.
She said her heart went out to the family.
