There is concern that small communities may end up bearing the financial brunt of possible changes to legislation covering wastewater quality.
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It estimates the cost to local authorities could be between $1.4 billion and $2.1 billion up to four times the estimated cost of fixing New Zealand's drinking water system.
Water New Zealand CEO John Pfahlert says these costs are alarming because many local authorities currently fail to meet their existing discharge consents, let alone new freshwater management requirements.
He says half the wastewater in this country is discharged into fresh water and more than half of that water comes from settling ponds which produce poor quality effluent compared to more modern mechanical systems.
John Pfahlert is worried that small communities would face the biggest financial challenges.
"The report says the average cost of upgrading wastewater treatment plants across New Zealand would be $1138 per household over 25 years," he said.
"But for people who live in communities of 500 or fewer people, the cost would balloon to $3576 per household," said Mr Pfahlert.
Of all wastewater treatment plants, 82 percent require upgrading for servicing communities of 500 or fewer people.
"It is clear that there is an urgent need to upgrade many wastewater treatment plants and a serious need to find an equitable way to share the costs across communities," he said.
"Improving the quality of wastewater to an acceptable standard will be even more costly than fixing our drinking water system.
"That is why we would urge the Government to address the delivery of all three waters drinking, storm and wastewater when it embarks on its reforms."