Following a complaint to the authority by Nathan's mother Angela Middlemiss, the case was re-examined and a manslaughter charge was laid against a caregiver in May this year - only to be withdrawn a few weeks ago.
Ms Middlemiss today welcomed the findings but said it did not send a strong enough message to those who looked after society's most vulnerable.
"I'm happy about the findings from today's report but I'm also devastated because it's a bit too late," said the grieving mother.
"There's no justice done for my son's death and it hurts our family very, very much because we've lost a beautiful child out of it."
She said it was important for the family and Nathan the case had its day in court and that hope had been extinguished after charges were withdrawn earlier this month.
"She [the caregiver] left a child in the bath unattended for 15 minutes that could not look after himself."
He was a 6-month-old in a 15-year-old body.
"The next case will be looked after a bit better but I needed it to be my son's case."
Ms Middlemiss said her teenager had gone to the Woburn Place facility for five years - but had she known of the danger he was in she would have taken him elsewhere.
"If I even knew that anyone was leaving him in a bath unattended I would have pulled him out of the site because that's dangerous."
She said the caregiver who was responsible for him that night was now no longer at the facility but still believed to be working in the industry.
She said the family wanted her to be held accountable and would be petitioning to have her name suppression order overturned.
They were also hoping to receive a personal apology from the detectives in charge of the case.
The IPCA said the circumstances of Nathan's death required a "category 2" homicide investigation and as a minimum a detective senior sergeant should have been appointed to lead the investigation.
However, against police policy a constable, Officer A, was assigned to investigate the death.
Less than a month after Nathan's death the investigating officers decided there was not sufficient evidence to prove the caregivers had been grossly negligent.
A detective senior sergeant reviewed the case and backed the call against laying any criminal charges.
But on review police charged Ms X with manslaughter.
However, in November the Crown Solicitor asked leave to withdraw the manslaughter charge and it was withdrawn in the High Court at Palmerston North on December 7.
Central District commander Superintendent Sue Schwalger today said the police had made a number of changes since the investigation into Nathan's death."Nathan's death was a tragedy and a great loss for his family.
Their distress has been exacerbated by the brevity of the initial investigation, and I apologise on behalf of police for that," said Ms Schwalger.
"It is vital that police policy regarding investigations into suspicious deaths, or deaths potentially involving criminal culpability, is strictly complied with. I have taken steps in my district to ensure that compliance, and to ensure that all such investigations are overseen by a senior detective."