Coroner Marcus Elliott acknowledged the stress on the family members who had waited years for an inquest, to look into, in the first place, how the boy died, and in a second phase due next year, at the role of child protection authorities who family members say failed them.
The boy was found dead in his bed by his mother in October 2015; she had not checked on him the night before when she got home, after he had spent the day in the care of her boyfriend at his home.
Police said they found meth pipes and ecstasy pills at the property.
A pathologist told the court the boy had "uncommon" injuries to his upper spine caused by his head being forced down, that strongly suggested contact with a smooth surface such as a carpeted floor or upholstered furniture.
"The amount of force required to basically crush fractures in those vertebrae has got to be really great. You really would have to have quite a strong pushing force to make that happen."
The injuries were "most unlikely" from falling backward, though they could result from someone falling on the child, or if he was forcibly thrown or struck vigorously, the pathologist said.
Fluid from the lungs on the bed indicated the toddler probably died within 30 minutes to an hour.
"It strongly suggests that he's been lying there for a period at least tens of minutes in the process of dying."
The court heard from the investigating police officer that the boy had previous fractures and injuries that were suspicious.
"There is a constellation of peripheral bony fractures of varying ages which are very unlikely to all be due to accidental injury," the officer said.
There was no evidence the mother was responsible for the injuries, the officer said.
The court watched two police interviews of the man. In the first, he told them he did not know what had happened.
"I haven't touched him. The postmortem is wrong," he said.
The video showed him agitated, rubbing his head and crying, and repeatedly standing and saying he wanted to leave.
"How do they know it was a blow to the head, not a fall?" he asked the police officer at one stage.
Shortly after, in a second interview, the man changed his story, saying instead he had been carrying the infant in the backyard.
"Tripped over the skateboard outside. And I fell on top of him.
"He was still alive, he seemed all right. He was still playing. Could he have died from that?"
The pathologist said it would have been clear to anyone looking on the boy was "immediately and obviously severely injured".
Had he not died, he would have been at least a tetraplegic, they said.
Police said they found a skateboard, with cobwebs on it, in the garage.
The officer asked the man why he did not tell them before about the fall.
"I didn't think it was relevant because he seemed all right," he replied.
Police then sent on to him a text to him from the mother, and asked what she had said to the man.
"'What did you do to my boy?'," he replied.
The police officer was asked at the inquest if he had any doubt the man killed the toddler.
"No," he said.
The coroner is yet to release any findings.
- RNZ