"We are satisfied that the Resource Management Act and the Fisheries Act are intended to work in tandem," the decision said.
Hawke's Bay Regional Councillor Neil Kirton said commercial and recreational fishers could win from the decision.
"Centralised resource management from Wellington has proven a disaster and this opportunity must be taken," Mr Kirton said.
"The decision puts protecting the region's fish and marine resource in our hands."
He said he would ask the council to immediately consider control measures, including a depth limit for fishing snapper.
"Such measures could be included in the draft Hawke's Bay Regional Coastal Marine Plan. This would give everyone the chance to debate introducing controls with a real chance that they can be implemented," Mr Kirton said.
Hawke's Bay Regional Council strategic development manager James Palmer said central government views were being sought "given the Government has yet to formally respond to its consultation earlier this year on the future of marine protected areas".
He said the Regional Coastal Environment Plan became operative in 2014 and was not scheduled for review until 2020/21. It contained a number of special conservation areas "which may be suitable for greater protection if the law allows".
"A change in the legal framework or interpretation of the law may result in the Regional Planning Committee wanting to expedite consideration of extra protection for the special conservation areas," Mr Palmer said.
"We are currently facilitating a group of fisheries stakeholders that is seeking to better understand the state and trends of fisheries in Hawke's Bay. We are currently developing a marine research plan with the group. This marine research will help identify new management measures that need to be taken, and this could include marine reserves."