Auckland's beach warning system has abandoned orange lights, saying beaches are either swimmable or not swimmable with no room for a "swim with caution".

The change means Auckland has departed from the guidelines run by a national consortium of regional councils and government agencies, Land Air Water Aotearoa (LAWA).

But the Auckland agency Safeswim, run by Auckland Council, Auckland Regional Public Health and Surf Life Saving's northern region, says people did not know what the orange light meant.

"We felt it was causing confusion because we got a lot of contact from people last summer that indicated that they regarded it as a public health warning, a high risk," said programme manager Nick Vigar.

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"[But] there are no different health advisories for green and amber. From a public health perspective there is no different advice."

Independent microbiologist Gemma Allen accused the agency of "trying to cloud the clarity of information" by making it look as if more beaches were safe for swimming.

"There have been a few improvements in small things," she said. "But generally there has been no real indication of enhanced sewage/stormwater flows."

Guidelines which have been in place since 2003, and are still stated on the LAWA website, provide a three-stage beach warning system:

Green: Below 140 enterococci per 100ml of water - "Suitable for swimming".

Orange: 140-280 enterococci per 100ml - "Caution advised. This site met the water quality standards for faecal indicator bacteria. Caution is advised for the very young, very old or people with compromised health."

Red: Over 280 enterococci per 100ml - "Not suitable for swimming."

Safeswim has dropped the orange light, and now grades any beach below 280 enterococci per 100ml of water as green, but has added a black symbol which will be used when there has been an actual sewage overflow.

Professor Gillian Lewis, a University of Auckland microbiologist who was consulted about the change, said Safeswim had adopted a system of modelling likely pollution levels at each beach given how much rain had fallen and other factors.

"Safeswim is not based on actual sampling of the water now," she said.

"What used to happen is we used to sample on a Tuesday or a Wednesday and use that to predict the water at the weekend. The accuracy of that was about random, actually.

"With the model, we can be accurate and we have done this with a series of tests. What we have found now is that the models are able to predict bacteria with 60 to 80 per cent accuracy."

Vigar said the orange light was used under the old system to tell the authorities that they needed to test the water again whenever enterococci exceeded 140 per 100ml of water.

"It's a signal to the regulatory authorities to say you might need to look into this," he said.

"It will continue to be in the information that we report to LAWA."

The 2003 guidelines, published by the Ministries of Health and Environment, said swimmers faced less than a 2 per cent risk of illness in sea water with less than 280 enterococci per 100ml, but did not specify any risk of illness in the "amber" range of 140-280 enterococci/100ml.

Niwa principal water quality scientist Graham McBride is reviewing the guidelines.

An evaluation of Safeswim published in March found that the current green, amber and red framework was "a good example of colour use to convey meaning".

It said beach users "would benefit from further simplification of messages" about how to respond to the colours, "notably the amber rating". But it did not recommend removing it.