There are fears the Mair Bank pipi beds might not recover from whatever has caused the shellfish population's crash to only one per cent of what it was a few years ago.
Local iwi and industry are also worried that if the sandbank changes shape as a result it will affect the harbour entry's shipping channel.
The number of pipi on the sandbank jutting into the Whangarei Harbour entry off Marsden Pt has fallen from an estimated 10,000 tonnes to less than 100 tonnes since 2005. The failing shellbank is of concern to local hapu Patuharakeke because of its valuable kaimoana resource and for cultural reasons.
But Mair Bank creates and protects one side of the shipping channel and, possibly without the tiles of shells holding it together, the sandbank might be changing structure. Those changes could affect tidal action on the Marsden Pt foreshore, as well as compromise the busy shipping channel.
"The bank is of major importance regarding the integrity of the channel, so it's important for a number of reasons we find out what's happening out there," said Juliane Chetham from Patuharakeke Trust Board.
Patuharakeke has led concerns about the collapsed pipi beds and Refining NZ, Northport, Northland Regional Council and the Ministry of Primary Industries are all now working with the hapu on the problem.
A ban on collecting pipi from Mair Bank was imposed late last year in a joint move by the ministry and Patuharakeke. That ban came three years after the hapu imposed a similar rahui at the smaller Marsden Bank, which is adjacent to the shore and accessible by foot or vehicle. The ban was based on concerns the Marsden Bank was being over-harvested before juvenile shellfish could grow.
"But Marsden has shown no sign of recovering in that time," Ms Chetham said. "In 2012 it was brought to our attention that Mair Bank is in trouble. It's a huge concern for us. On October 1 last year we closed Mair Bank to commercial, recreational and customary take too. We were not able to discern whether there had been a virus or some other natural catastrophe but it seems there has been some event or a combination of environmental factors."
Northport chief executive Jon Moore said the company carried out regular hydrographic surveys in the area but would welcome a full study into the pipi bank's demise.
Mr Moore said the port had "a fail-safe" waste water storage set-up that, in the 13-years since it was built, had never breached its consent requirements.
"We're very confident we're not having any impact [on the pipi bed]," he said. "If [the cause] was toxic it would have to be catastrophically toxic and there is no evidence of contaminants or other effects."
Scientists believe it is unlikely the huge pipi biomass collapsed through over-harvesting but Niwa biologist James Williams said the data behind a "desktop" review and report done for NRC last June was limited.
"It wasn't possible to pinpoint a cause. Contaminant levels were low, there's no evidence of disease, no outbreak of pipi predators. It is difficult to know what has been happening. I would hope this will lead to a full investigation."
The absence of juvenile shellfish coincided with the bank rising in steepness and height and retreating at its seaward flank, Dr Williams said.