English says threat ‘speculative’ and impact uncertain.

The Government has dismissed one of the key recommendations in a report on rising sea levels despite a warning that 9000 homes around New Zealand are sitting precariously close to the high water mark.

Parliamentary Commissioner for the Environment Jan Wright took the rare step of making a specific warning to the Finance Minister in her latest report on the threat of rising oceans driven by climate change.

The commissioner said the Government needed to start preparing for the huge potential cost of higher sea levels, which could lead to damage of between $3 billion and $20 billion in replacing buildings alone.

Finance Minister Bill English immediately said he would not be taking up the recommendation. Sea level rises were just one of several risks, he said, and would not specifically be factored into the Government's planning decisions about infrastructure.

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He described the commissioner's findings as "speculative" and said there were still many uncertainties about the potential impacts of rising oceans.

In her report, Parliament's environmental watchdog concluded that central and local government needed to completely overhaul the way they were preparing for rising sea levels.

"Continuing sea level rise is not something that might happen - it is already happening, will accelerate, and will continue for the indefinite future," Dr Wright said.

A total of 9000 homes were less than 50cm above spring high tides. Thousands more were within 1m of this threshold.

Of the major cities, Auckland and Wellington had relatively few homes in low-lying areas.

But Christchurch had nearly 1000 just above the spring high tide mark, and Dunedin had 2600 within the 50cm threshold.

Five coastal towns - Napier, Whakatane, Tauranga, Motueka and Nelson - had more than 1000 homes between zero and 150cm above the high water mark.

The report predicted sea level rise of 30cm over the next 50 years in New Zealand.

That would mean 1-in-100 year flooding events would become annual events in Christchurch, and four-yearly in Auckland.

The report said sea level rise was caused by warming, expanding oceans, the retreat of glaciers, and shrinking polar ice sheets.

The most difficult aspect of preparing for higher seas would be dealing with New Zealanders' coastal properties.

Dr Wright said councils would need to use science fit for purpose, and engage with communities "in a measured way and with empathy".

The process in Kapiti and Christchurch had been particularly "adversarial", she said, as local government had clashed with residents over plans to prepare for higher sea levels. Councils also needed better direction from central government.