The trust had sought to introduce fishing controls on and around Astrolabe Reef after the reef ecosystem suffered from the impact of the grounding of the Rena in 2011.
It argued the ecosystem had begun recovering after an exclusion zone was placed around the reef immediately after the grounding, but the gains had been wiped out since fishing recommenced in April 2016.
Justice Whata said the Fisheries Act was focused on biological sustainability of the aquatic environment as a resource for fishing, whereas the Resource Management Act had a broader definition of the protection of ecosystems.
His judgement set aside the Environment Court declaration, although he said his reasoning accorded in many respects with the court.
Justice Whata said the Environment Court decision placed no limit on the extent to which a regional council could control fishing, provided it was a specified and dominant resource management purpose.
He has given the parties to the High Court action three weeks to make submissions on his suggested declaration.
It said a regional council must not use its powers under the RMA to manage the utilisation of fisheries resources. Neither could it manage the effects of fishing on the sustainability of the aquatic environment as a resource for fishing needs.
Justice Whata said a council could manage fishing effects not directly related to the sustainability of the aquatic environment as a fishing resource. Maintaining indigenous biodiversity was permitted within the coastal marine area, "but only to the extent strictly necessary to perform that function".
He used evidence from the Environment Court to illustrate where the line could be drawn for a council to control other effects of fishing on the environment.
An expert witness used the impact of crayfish and snapper fishing on the Bay's shallow rocky reef ecology. They were major predators of kina but where too many were taken, kina multiplied and ate the kelp forest. This led to virtually bare rock areas abundant with kina.
Justice Whata said it was not enough to simply assert that additional control over fishing was appropriate to protect marine vegetation. It would need to be assessed if it was permissible, given the sustainability of marine vegetation as a fisheries resource was secured by the Fisheries Act.
He envisaged a symbiotic relationship between the RMA and Fisheries Act, with some flexibility to meet "exigencies".
Symbiotic relationships were essential to many organisms and ecosystems, providing a balance that could only be achieved by working together.
Supporters of regional councils being able to impose fishing controls:
- Motiti Rohe Moana Trust
- New Zealand Maori Council
- Ngati Makino Heritage Trust and other iwi
- Royal Forest and Bird Protection Society