Conservationists and the opposition say government's changes to clean water standards are a "shambles" and "trickery", after an official report found the new rules may weaken some regulations.

The National Institute of Water and Atmospheric Research (Niwa) this week released its report into the government's proposed changes to freshwater management policy.

It found although the new standards were tougher than the 2014 standards for boating and wading quality, they lowered the standard for the "minimum acceptable state" for swimming.

However, the report did note the 2014 swimability standard was "very high" - equivalent to an "excellent" grade under European Union standards.

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Minister for the Environment Nick Smith on Tuesday said the government would be reopening submissions on the proposal to the public and extending the deadline for scientific reports on the details of the grading outlined by Niwa.

Environmental lobby group Forest and Bird said the consultation process has been a "complete shambles from start to finish".

"The proposed changes to the swimming standards were rooted in a marketing ploy, not scientific rigour," freshwater advocate Annabeth Cohen said.

"This new analysis is an example of the scientific research that should be carried out before policy is made, not after submissions have closed."

Labour environment spokesperson David Parker said Niwa's report contradicts statements by the government.

"It's time to stop the trickery," he said.

Since the proposal was announced this year - with the aim of getting 90 per cent of lakes and rivers safe for swimming by 2040 - the government has denied the goalposts had been shifted, saying environmental groups were confusing different standards.

Smith said the Niwa report would help inform the plan going forward.

"The grading system has generated significant debate and these reports provide more information on how the grading system compares internationally and the level of precaution they are based on," he said.

The reports also confirmed that changes to the National Policy Statement would allow a significant improvement in the microbiological water quality of waterways, he said.