New housing and hotel developments cannot be stopped until sewage stops flowing into the Waitemata Harbour, says Auckland Mayor Phil Goff.

He was responding to "dangerously high" levels of bacteria indicating the presence of faeces found at two sites in Auckland's inner suburbs following water quality tests conducted by the Herald's Focus team.

Goff's answer is to progress a $1 billion "central interceptor" pipe that will cut overflows into natural waterways by 80 per cent. Work is due to begin in 2019 and be finished about 2025.

Asked if he was prepared to see things get a little worse in the meantime before the central interceptor starts operating, Goff said the city cannot stop building hotels when there was a shortage of hotel space and stop building new houses when there was a housing crisis.

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Besides, he said, it was unfair to blame new buildings, constructed to strict compliance standards, when 16,000 old houses connected to the old combined sewer-wastewater pipe are causing the problems.

"The solution is not to stop building any new houses in any of those areas in Auckland, it's to fix the problem by getting a central interceptor that has the capacity to cope," Goff said.

The mayor said he had to deal with both problems, housing and overflows, and would deal with them simultaneously.

Goff said he had talked with Watercare boss Raveen Jaduram, who criticised Auckland Council for allowing developments to occur knowing there is no adequate stormwater system and this will result in more frequent harbour spills.

"What I don't want is Watercare and stormwater Auckland pointing the finger at each other and saying it is your responsibility."

Goff claimed Watercare, responsible for wastewater, and council, responsible for stormwater, were working constructively together on an "optimisation plan" to get the best results as quickly as possible.

"I don't care whose fault it was in the past. I want this problem fixed now and I want them to collaborate to do it," said Goff.