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Associate Prof Nicolas Cullen and senior lecturer Daniel Kingston have described the predictions by Jim Flynn as ``very unlikely''.
However, the Insurance Council of New Zealand has confirmed Prof Flynn's suggestion insurance companies are unlikely to cover sea-level rise in their policies in future.
On Monday, Prof Flynn told a Dunedin City Council public forum huge erosion of polar ice that had begun in 2014 meant predictions on the rate of climate change had changed.
He said there were 1932 homes in Dunedin, mainly in South Dunedin, built below 25cm, and a 25cm sea-level rise could occur before 2034.
He said by 2090, South Dunedin would be under 5m of water, along with Forsyth Barr Stadium, the Otago Polytechnic and other low-lying areas.
But approached for comment on the predictions, Prof Cullen and Dr Kingston disagreed.
Prof Cullen, whose expertise includes glaciology and climate change, said Prof Flynn's figures were ``questionable''.
He said the observed sea-level rise was 3.4mm a year, which was ``quite high compared to historical estimates''.
If that rate continued for the next 20 years, there would be a total 68mm sea-level rise - ``quite different''from Prof Flynn's estimate.
``I agree that there is evidence that the two large ice sheets [Greenland and the Antarctic] may contribute more to sea-level rise in the future than previously thought, but I would think it is very unlikely that South Dunedin will be under 5m of water in 2090.''
Dr Kingston, whose expertise includes atmospheric circulation patterns and climate change, said he agreed with Prof Cullen.
``The numbers in that article, like 5m by 2090, are at the very, very extreme end of what's likely.''
To Prof Flynn's suggestion the more recent erosion of polar ice had changed what could be expected in terms of sea-level rise, Dr Kingston said, ``I don't think the matter is settled by any means.''
A rise of 5m would mean the entire West Antarctic ice sheet disappearing, or the entire Greenland ice sheet disappearing.
``The likelihood of that happening by the end of the century is low - not impossible - but the real extreme end of the situation.''
Otago Regional Council chief executive Peter Bodeker said he was not sure if the issue would become a serious problem in 25 years, 50 years or 75 years.
The ORC and the Dunedin City Council were working together to identify options to adapt to issues in South Dunedin.
``What we are saying is it is coming,'' Mr Bodeker said.
``I think everybody agrees it is coming and we've got to start planning sooner rather than later.''
The ORC used data from the National Institute of Water and Atmospheric Research, and took its own measurements.
Measurements in the harbour had been done for some time, ``which is why we know there is sea-level rise''.
There was also a sea-level recorder on Green Island, and three bore sites in South Dunedin to measure ground water.
Prof Flynn's predictions were ``a different timing to ours'' but, irrespective, it was important to start making some progress.
That was what the councils were doing with their work.
On Monday, Prof Flynn said Australian insurance companies were already excluding sea-level rise as a risk covered in their policies.
That would extend to New Zealand and could make at-risk homes uninsurable in the Dunedin area in the next five years, he said.
Asked about the issue, an Insurance Council of New Zealand spokeswoman said that, generally, actions of the sea and coastal erosion were typically excluded from Australian household insurance policies.
``There are a small number of insurers who will cover actions of the sea, but it is rare.''
Asked if New Zealand was going in the same direction, she said insurance covered sudden and unforeseen events.
``Sea-level rise is not sudden and unforeseen.''
Dunedin South Labour MP Clare Curran said she found Prof Flynn's claims ``very alarmist''.
``Can we please be sensible about this?''
Ms Curran said insurance companies took a sensible approach to the issue.
Prof Flynn responded last night he trusted projections by the Earth Sciences Department of Oxford, ``so we can disagree about 2090''.
He rejected a formula Prof Cullen sent the Otago Daily Times to back his argument, saying it was ``simply mistaken''.