The neighbouring Te Huruhi Primary School tested positive for E. coli two weeks ago.
The Ministry of Education is responsible for Waiheke High School's water treatment infrastructure but the high school manages both water supplies using operations' grants from the Ministry.
Young told the Herald parents were alerted by email on Wednesday. None of the high school's pupils had become sick but she would not comment on the situation at the neighbouring primary.
The Ministry of Education was alerted to the contamination last night and is working with the schools. The cause of the contamination is unknown.
Katrina Casey, the Ministry's deputy secretary sector enablement and support, said a new treatment plant had been installed at the school.
"Waiheke High is also installing 2 Ultra Violet units to remove e-coli bacteria, in addition to new filters. Te Huruhi has, in addition, cleaned and treated its water tanks."
Both schools were shipping in bottled water on a daily basis, with management instructing teachers and pupils to use hand sanitiser.
The Ministry was continuing to test the water quality and over the past year had been helping the school upgrade its water system, a task which included replacing the bore in August 2017 and repairing leaks earlier this months.
"These are water quantity issues which are not related to today's information about contamination," Casey said.
"We are supporting both schools to address this issue, with funding and contractors, to ensure the Health and Safety of all occupants of both schools."
E. coli-related illness can cause stomach pains, mild to severe diarrhoea, vomiting and fever.
Symptoms can be severe for children, elderly people, or those with weaker immune systems.
Young said the high school's water testing was clear when Te Huruhi Primary School's water tested positive a fortnight ago.
She would not comment on the primary school's process after the readings came back.
Young and Te Huruhi's principal, Adam Cels, said in a joint statement the health and wellbeing of students and staff were the school's top priority.
"As soon as we were aware of the situation we informed our community. We also informed the District Health Board and the Ministry of Education. We are all working to rectify this issue as soon as possible.
"In the meantime we can confirm that this is not impacting on our students and their learning, that everyone has access to drinking water, and all steps are being taken to ensure this does not affect the health of our students and staff."
The high school has a roll of 517 students while the primary school has 389.
The Ministry of Health said the matter would be handled by the Auckland Regional Public Health Service, which did not respond to Herald inquiries last night.
The discoveries come not long after E. coli was found in Lower Hutt water.
Chlorine has been added to Lower Hutt's water supply after a reservoir tested positive for E. coli earlier in the year.
Hutt City Council said it started chlorinating the supply for 76,000 residents after a routine test from the Naenae reserve came back positive.
Before that, an outbreak of gastroenteritis in Havelock North in August last year was linked to E. coli contamination.
About 5500 people, or a third of Havelock North's population, fell ill after drinking water contaminated with campylobacter.
The illnesses was linked to three deaths, and three people contracted Guillain-Barre Syndrome, a neurological disorder.
It was confirmed earlier this month that the most likely source of the contamination was sheep faeces that ran off a paddock following heavy rain.
What is it?
E. coli are bacteria normally found in the gut of warm-blooded animals and people.
There are many harmless types of E. coli but some types that can cause disease.
Illness-causing E. coli can be transmitted through contaminated water or food, or through contact with infected animals or people.
It can take about 2-10 days for symptoms to show after the bacteria is ingested.
What are the symptoms?
If someone contracts an E. coli related illness, they can experience stomach pains, mild to severe diarrhoea, and vomiting, as well as a possible fever.
Symptoms can be severe for children, elderly people, or those with weaker immune systems.
When to go to the doctor:
Most symptoms last from a few days to a week. Contact a doctor if:
• You have diarrhoea that isn't getting better after four days, or two days for a child.
• You have a fever with diarrhoea.
• If stomach pains don't improve after a bowel movement.
• If there is pus or blood in your stool.
• If you can't keep liquids down well.
• If you have been vomiting for more than 12 hours. If a baby under three months shows symptoms, contact a doctor immediately.
• If you become extremely thirsty, dizzy, or have a lack of urine. These could be symptoms of dehydration.
