A forensic pathologist has told the coroner it was more probable than not that Lachlan Jones drowned.
The 3-year-old was found unresponsive in Gore District Council oxidation pond on 29 January 2019, just over a kilometre from his mother's house, where he lived.
Two police investigations found the boy accidentally drowned.
But his father Paul Jones did not accept that and told the coroner during the first phase of the inquest in May that officers botched the case.
The inquest into his death resumed this week, entering its second phase.
Dr Judy Melinek, who previously worked to identify victims of the 9/11 terror attacks, was asked to review the findings of the pathologist who initially determined Lachlan drowned.
During the three-week long first phase inquest, Paul's lawyer Max Simpkins advanced the theory Lachlan's mother Michelle Officer and her two older sons killed the boy, before storing his body in a freezer and then dumping it in the sewage pond.
At that inquest, the pathologist who carried out the post-mortem said it would have been easy to identify if he had been put in a freezer and Lachlan's body showed no signs of that.
He found nothing suspicious nor surprising during his exam.
There were no signs of external trauma, said the pathologist, who had interim name suppression. But he accepted a more thorough forensic autopsy should have been carried out considering the concerns about Lachlan's death.
Dr Melinek on Wednesday told the inquest she agreed a forensic autopsy should have taken place but even in its absence there was enough evidence to safely conclude Lachlan drowned.
"After reviewing the referenced sources in this case, it is my opinion that the scene investigation by police and the post-mortem examination ... indicate with reasonable medical certainty that Lachlan Jones died from drowning," she said.
"There is no evidence of physical abuse to indicate that this death was intentionally inflicted. The autopsy pathologist's post-mortem examination was incomplete given that the coroner's written direction was for a full autopsy - not a lesser post-mortem exam.
"[The pathologist's] decision to perform a lesser exam, however, was made out of deference to New Zealand cultural practices, and he was unfortunately not notified of any suspicious circumstances by the police or coroner that would have caused him to decline the case."
The police officer who found Lachlan's body in the pond noted foam around his mouth which needed to be cleared before beginning resuscitation efforts.
Dr Melinek said that presented a clear sign of drowning.
"In drownings the decedent will breathe in water, and while breathing the inhaled water gets frothed up because of a protein (surfactant) lining the airways. The presence of foamy material seen at the mouth of the deceased at the scene prior to the initiation of CPR and the aspiration of foreign material on microscopic sections of the lungs with visible pulmonary oedema, indicate that the child breathed in water, and likely drowned.
"If the child had had lethal traumatic injury that caused death prior to entering the water then I would not have expected the police to notice foam at the airway prior to the initiation of resuscitation. The police investigation, scene and circumstances all point to drowning as the primary cause of death and there is no external injury that raises any concerns of other-person involvement in this child's death."
During questioning she conceded foaming of the mouth was also possible in the cases of traumatic brain injury, but she would have expected evidence of such trauma to be obvious if that was the case.
Any other conclusion was speculative as there was no evidence pointing to another mode of death, Dr Melinek said.
Retired crime scene investigator takes aim at police narrative and evidence
Retired American crime scene investigator Karen Smith took aim at New Zealand Police, their narrative and the evidence of Lachlan's mother while giving evidence on Wednesday afternoon.
"I have read many articles related to the excellent work that the New Zealand Police have done and can do," Smith said.
"I reference the ongoing investigation into the disappearance of Amber-Lee Cruickshank by Inspector [Stu] Harvey (the officer in charge of the reinvestigation into Lachlan's death) and his team. Their efforts since 1992 have been tenacious and admirable and I hope with all my heart that Amber Lee's case will be solved.
"What I cannot understand is the continued obstinance and refusal to put that same effort into answering the ongoing and remaining questions about the death of Lachlan Jones. Lachlan deserves no less."
A key piece of evidence at the first phase inquest was the recollection of Deborah Thurston, a neighbour of Lachlan and his mother.
Thurston told the inquest she heard Lachlan banging around her washhouse on the night he went missing and hours after he would have been dead in the alternative possibility.
Thurston never saw Lachlan, but was confident she had heard him and saw Officer keeping an eye on her son.
But Smith today dismissed her recollection.
"Based on the available statements, omissions, evidence, and subsequent analysis of time, distance and speed - the results are inconsistent with prior reported escapes and Ms Officer's ability to catch Lachlan and regain his care and control," Smith told the coroner.
"The results and available information do not support the reported circumstances.
"Based on the available information, it is my opinion that Lachlan Jones was not present at Ms Thurston's house."
She was also not convinced of the importance of foam seen around Lachlan's mouth by the police officer who found him.
"The investigators should have considered the possibility that a small amount of white foam could be a consequence of chemicals present in the pond water. Water samples taken on the night may have answered this question via laboratory analysis, as well as a comparison to biological samples obtained from Lachlan during a forensic postmortem. No foam or water was present in the photographs taken at the morgue," Smith said.
"I have cleared the foam cone and water from a drowning victim to clear the airway for CPR. It is a futile effort. Every immediate drowning victim that I have encountered in my career has had a continuous cone of blood-tinged foam emanating from the mouth and nose when recovered from the water...
"While experience alone is certainly not enough to opine conclusions regarding every theoretical possibility, experience does inform inferences and logic and does help to formulate associated questions regarding the known circumstances and available evidence.
"I defer to a forensic pathologist for further determination and a conclusive opinion about the lack of a foam cone and water after Lachlan's immediate recovery."
The inquest was set down for two weeks.