Lachlan Jones was found unresponsive in Gore District Council oxidation pond on January 29, 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 inquest in May that officers botched the case.
"I don't know what's happened on this day. I don't know how my son got out there. I'm here to find the answers," Jones said, during a tense exchange with the lawyer for police Robin Bates.
"It just seems like a bloody botched up police job and you're trying to fix it."
During the three week-long first phase inquest, Jones' lawyer Max Simpkins raised the prospect 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.
The two-week second phase inquest would hear from several expert witnesses, including a retired American crime scene investigator, and one of the Lachlan's half brothers was due to again take the stand.
