The trust applied for consent to rebuild the old wharf that was demolished in the 1950s. The project would have turned the wharf into an educational, observation and information centre focused on birdlife and local history.
In rejecting the consents, the independent commissioners said the rebuild had the potential to impact the habitat of the critically endangered fairy tern.
The New Zealand Fairy Tern Charitable Trust, Department of Conservation, and Forest & Bird were among those opposed to the rebuild and called expert witnesses to back up their arguments.
But trust chairman Colin Leach said no evidence was presented at the hearing that showed increased human activity on the harbour and foreshore over the past 20 years has affected the fairy tern population and its capacity to breed.
"Successful foraging areas exist in other parts of the harbour with much higher levels of human activity than the area of the proposed wharf. Much of the evidence presented was contradictory and opinion rather than fact or science."
Leach said the decision was a great disappointment for the project team, who had worked hard for the last four years and with community support, funded the bulk of resource consent costs of more than $120,000.
"Half of this cost, some $60,000, relates to NRC charges. The trust, as a volunteer-driven charity, applied for relief from these costs and was generously given a refund of $896. It is hard to view this without a great deal of cynicism."
He said the decision deprived a growing community a much-needed amenity, which ironically would allow people to walk out over the foreshore and water without interfering with birdlife.
"Mangawhai residents and visitors have every right to be angry and concerned because if the NRC are consistent with this decision, then swimming, walking and launching boats on the intertidal area would be completely banned."
In attempting to reach common ground, Leach said the trust offered a number of mitigating changes to their application, including removing the gangway and pontoon, which effectively turned the wharf into an educational, observation and information centre for birdlife and local history.
These were rejected by the commissioners in what seemed like a predetermined position, he said.
NRC group manager regulatory services Colin Dall said the council understood that any consent applicant that has their consent application declined would be very disappointed.
"As the decision to decline the Mangawhai Historic Wharf Trust's consent application is still subject to appeal, it is inappropriate for the council to respond to the Trust's views on the matter other than to say that in forming a view on the decline of the application it is important to read the independent hearing commissioners' decision."