A decision to decline a controversial water conservation order on part of a Hawke's Bay river is being challenged by Forest and Bird, which says it sets a "dangerous precedent".

Earlier this year, the Environmental Protection Agency recommended a WCO be put in place on the upper section of the Ngaruroro River (the headwaters to the Whananwhana Cableway).

But the agency declined an application for a WCO on the lower section of the river.

Forest and Bird, one of the original applicants, have now submitted what it is calling an appeal on the EPA's recommendation to decline the WCO on the lower section of the river.

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Forest and Bird Regional Manager Tom Kay said the "wrong legal test was applied" by the EPA.

"The tribunal accepted the outstanding value of the lower river for native birds but they haven't made any provision to protect it – which doesn't make sense to us."

He said the tribunal said an outstanding value needed to be threatened before a WCO can be applied.

"We think that's absolutely incorrect.

"Recognising an outstanding value is what a WCO is for, regardless of whether there is an immediate threat to that value."

He said Forest and Bird wanted its submission to help show that the "threat test" is unwarranted in considering WCOs.

"If left unchallenged, the tribunal's recommendation could set a dangerous precedent for future WCO cases."

He said a WCO would indefinitely protect the lower Ngaruroro in future decision making processes.

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"No other plan or document can match that level of protection for a river."

Hawke's Bay Regional Council, which opposed the WCO, said it was satisfied with the tribunal's finding on the upper river, but has lodged a submission seeking clarification on how the Water Conservation Order's protections in the upper river will be enforced.

Group manager strategic planning Tom Skerman said the submission is confined to the workability of the provisions, as Regional Council is responsible for its enforcement.

"The Regional Council is not appealing the substantive findings and recommendations for the granting of a Water Conservation Order in the upper reaches and the rejection of an Order in the lower reaches.

"We are simply seeking some amendments that would clarify how to protect the outstanding values in the Upper Ngaruroro."

Protections recommended by the EPA for the upper section of the river include a ban on resource consents for dams and water takes which would deplete the river.

The original application was made by six groups: New Zealand Fish and Game Council; Hawkes Bay Fish and Game Council; Operation Pātiki Ngāti Hori ki Kohupātiki; Royal Forest & Bird Society of New Zealand; Whitewater NZ and Jet Boating New Zealand.