A massive pipi bed in Whangarei harbour is dying and there are fears the change could destabilise the harbour - and Marsden Point itself, Radio NZ reports.

The volume of pipis on Mair Bank has slumped from 10,000 tonnes to less than 100 tonnes, sparking fears the massive sandbank, which protects the harbour entrance, will disappear.

The sandbank, shaped similar to a shark's tooth, lies just off Marsden Point. Locals previously waded out at low tide to scoop up the daily limit of 150 of the shellfish in a couple of minutes. But no more.

NIWA fisheries scientist, James Williams, said the decline had been drastic. Over the last four to five years the pipi population has collapsed.

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He said the bank had been eroding from the south and gaining height; coinciding with an apparent absence of juvenile pipi.

"There was a huge biomass there of pipi, everywhere pretty much on the bank and sub-tidally of about 10,000 tonnes and that's been reduced to less than 100 tonnes from the 2014 survey," he said.

"So, less than one per cent of what there was in 2005."

Dr Williams said pollution had not been a problem. Regular testing shows the water quality is very good, despite the presence of the oil refinery and the timber port next door.

Mair Bank was closed to pipi pickers last year but Dr Williams said the volume of shellfish being taken, including a commercial catch, was miniscule compared to the vast quantity available.

He said it might be worth testing the water to rule out pollution by terpenes -- compounds found in pine logs. Dr Williams said it was not known what impact the compounds might have on pipi, but they could act as pesticides on some species.

However, Northport chief executive Jon Moore said run-off from the port's log storage area drained to a big settlement pond.

"It can pump to the harbour if it reaches a high level, so if you have a storm event, obviously the last thing you want is all of that overflowing so there's a pipeline back to the harbour," he said.

"It pumps on those high rain events, but at that point when you've got a heavy rainfall, most of the water that's coming through there is pretty damn clean anyway."

Radio NZ reports the refinery and Northport are worried the loss of millions of shellfish could destabilise Mair Bank.

The New Zealand Refining Company's environmental manager, Riann Elliot, said if the bank goes, there would be knock-on effects for the harbour and the foreshore.

He said the channel was "self-dredging".

"There's no maintenance dredging required here - that could be jeopardised, so the entry to the harbour could be jeopardised."

"Erosion along the foreshore along Marsden Point could change drastically. We've currently got a bit of an erosion problem and there's evidence to suggest that could accelerate."

New Zealand Refining chief executive Sjoerd Post said any increase in erosion had to be a concern for the refinery.

"Our site is very close to the sea perimeter, so the pipis dying out may cause instability in the bank which may lead to bigger consequences for us," said Mr Post.

"But first and foremost, we are really concerned around the fact that sort of an entire species seems to be dying out all of a sudden."

Mr Post said it was tangata whenua, Patu Harakeke, who first raised the alarm about the Mair Bank pipi beds.

New Zealand Refining and Northport back their call for urgent research into the problem.