Public health officials will know tomorrow if untreated water which flowed into Dunedin pipes last night was a major public health risk.

Photo: RNZ / Ian Telfer

Thousands of people in Dunedin have been warned to boil tap water until at least Friday, after water from the disused Ross Creek reservoir was mistakenly let into the drinking water system.

Dunedin City Council said it issued the alert for the city this morning because of the potential health risk.

"Avoid drinking water from the public water system, but if you must do so please boil it first," the council said.

Check the latest advice from the council here.

There are fears of a repeat of the water contamination crisis which made 5000 people sick in Havelock North a year ago.

Dunedin Hospital has activated its civil defence bunker in case people present with vomiting or diarrhoea.

Otago University, also in the affected zone, advised staff and students to avoid drinking tap water on campus and in the North Dunedin area.

Photo: Supplied: Dunedin City Council

It cancelled all its public dentistry clinics until further notice.

The council started getting complaints yesterday about yellow or brown discoloured water coming out of taps in the North Dunedin area, it said.

Its chief executive, Sue Bidrose, said staff yesterday had needed to lower the level of the Ross Creek reservoir to assist with the dam refurbishment project there.

However, they inadvertently sent raw water through old pipes into the city's water supply.

The old pipes did not exist on any council plans, and were supposed to have been disestablished about 30 years ago, she said.

As soon as the council became aware of the problem, the pipes were shut off and the boil water notice was issued at 10am, Ms Bidrose said.

Infrastructure manager Ruth Stokes said three days of consecutive 'all clear' tests were needed, plus a further 24-hour period before the council could lift the boil water notice.

The first test results were expected tomorrow.

Ms Stokes said the council received 44 complaints of discoloured water by 11.20am today.

The warning covers the central city from the town belt to the harbour and the suburbs of North Dunedin, Leith Valley, Woodhaugh and the Warehouse Precinct.

1720 residential properties and 825 businesses were affected.

Five teams of council staff were releasing water from hydrants around the city to clear the pipes, the council said.

It had ordered several water tankers to distribute clean drinking water in the city.

More than 900 comments and questions have been posted on the council's Facebook page, with many people asking for more information on what caused the problem and the possible effect of drinking the water.

Essential info for affected residents:

Boil all drinking water. Tap water in affected areas must not be used for drinking, making baby formula and juices, making ice, washing fruits and vegetables, or brushing teeth.

Zips do not boil water sufficiently, water needs to be through a rolling boil for at least one minute and filtered water should also be boiled for at least one minute.

If you're in an affected area please flush run your taps for 10-15 minutes. This will flush the water and will help with the cleaning process.

If you have a water tank please empty it so it can be refilled with clean water.

If you are in an affected area and have water that you have drawn from the tap since yesterday, please tip it out and do not drink it.

As a precaution please use hand sanitiser after washing your hands. Care should be taken with bathing and showering so that water is not swallowed.

We are working on providing water tankers so there is a supply available. We will let you know where these will be and when.

Most coffee machines only heat water to 80-85°C. These machines need to be used with pre-boiled water. Plumbed-in machines should not be used.

Source: Dunedin City Council