In findings about the incident, released today, the Health and Disability Commissioner found responsibility for "deficiencies" in William Burton's care in lay with the Capital and Coast District Health Board.
It breached the Burtons' right to have "services provided with reasonable care and skill", the commissioner ruled.
The DHB undertook its own review into the handling of William and its findings are set out in the commissioner's report.
William, who is now 2, was brought to the hospital by his parents in October 2013 and was twice sent home within two days, with a junior doctor on the second occasion diagnosing a gastric illness.
Three days after that, on William's third visit to hospital, meningitis was diagnosed and his parents, Derek and Wendy, then spent a heart-wrenching month watching their boy's brain wither away.
The DHB's investigation found the second doctor to see William did not give the possibility of an infection proper consideration and the hospital did not have in place a proper process for more senior staff having oversight of paediatric juniors.
The DHB has since changed its practices, including making sure a child taken to hospital twice within 72 hours is examined by a senior staff member.
The health board has also apologised to the Burton family. It will assess the changes it has made in six months' time.
"CCDHB remain saddened by the significant neurological injury and permanent disability that resulted following William accessing our care," it said in the commissioner's report.
The second doctor to see William was now overseas, but the board said: "It's difficult to convey in writing the distress and regret felt after hearing of William's neurological injury. I have been deeply affected by the outcome on William's health and cannot begin to imagine how affected the Burton family must be."
An independent paediatric emergency specialist, reporting for the commissioner, found William's care adequate on his first visit to hospital, but he was concerned the boy was only seen by a junior doctor on his second visit.
That doctor also didn't give the Burtons clear instructions about what to do if William's fever remained, but their assessment was appropriate given their level of experience.
In a statement, Capital and Coast DHB chief medical officer Geoff Robinson said the DHB accepted the commissioner's findings and "unreservedly apologises for the grief and distress suffered by the patient and their family as a result of this regrettable event".
"As health professionals, patient safety is our number one priority and we have taken several actions following this event to reduce the risk of it occurring again," Dr Robinson said.
"A formal assessment and discharge process for patients seen by junior doctors has been developed to ensure greater clinical oversight from senior doctors. Any child who re-presents to hospital within 72 hours is now assessed by a senior doctor before discharge.
"We have increased staffing to ensure a paediatric registrar, a doctor who has at least three years' experience, is on duty 24/7. All paediatric medical staff must also now complete a best-practice guideline on feverish illness in children under five, from the UK's National Institute for Clinical Excellence."
