NIML general manager Steve Wells said the local business was "trucking as normal."
Aquaculture experts said the spat problems had highlighted the vulnerability of the industry, which is dependent on spat mostly washed up on Ninety Mile Beach. As part of attempts to address the problem, Sanford and the Ministry of Primary Industries this month announced the opening of New Zealand's first commercial mussel hatchery.
Graeme Coates, chair of the Bay of Connections Regional Aquaculture Organisation and a director of Aquaculture Direct, said the current situation was not in itself catastrophic, and that he expected it to be a one-off, with conditions improving in a year or so.
"The catastrophic thing is that we didn't start thinking about hatcheries years ago," Mr Coates said.
The water has been at higher than normal temperatures, which may have affected the spat survivability
He said the current shortfall was thought to be caused by recent warm water temperatures, plus a lack of rain washing nutrients into the sea.
"It probably means the mother mussel beds aren't producing as much. And they didn't ripen to the normal extent so the spat are not strong.
"The water has been at higher than normal temperatures, which may have affected the spat survivability."
The other major problem was that the industry was growing in a number of places around New Zealand and demand for spat was greater, he said.
"It means over the next 18 months there's going to be less spat seeded on the farms, so it means there will be fewer mussels in the market."
Chris Battershill, the Bay of Plenty Regional Council chair in coastal science, who heads Tauranga's Coastal Marine Field Centre, said the industry had become reliant on the wash-up in the north.
"When we think about New Zealand aquaculture, we really only have two major targets, mussels and salmon," said Dr Battershill.
"That's why we are concerned about threats to what is really still an emerging industry in this country, when you consider our marine estate.
Juveniles beached in North supply most farms
About 75 to 80 per cent of all New Zealand mussel farms are seeded with wild spat, which
wash up attached to seaweed on the shores of Ninety Mile Beach.
The balance is caught on spat-catching lines in mussel farms in Golden Bay, Tasman Bay and Marlborough Sounds. The spat are gathered under a licensed quota system by a number of independent operators in the Far North, said aquaculture expert Graeme Coates.
It means over the next 18 months there's going to be less spat seeded on the farms, so it means there will be fewer mussels in the market
The spat are produced by long-established mother mussel beds off the western coasts of New Zealand. The juveniles spend three to four weeks looking for a place to land and grow. Most end up on Ninety Mile Beach, with some from the West Coast finishing up in Golden Bay and Tasman Bay, where they are caught by mussel farmers on special lines.
In the past year, the spat have failed to show up on the Far North beaches, and there have been few caught in the South Island.
However, there are some encouraging signs. According to Chris Battershill, head of Tauranga's Coastal Marine Field Centre, the Eastern Sea Farms Ltd development in Opotiki had experienced natural and strong spat-fall over the past year or so.
ESFL is owned by the Whakatohea Trust and Sealord, "The farm there is new and the origin of these juveniles is unknown," said Dr Battershill.
"But it looks like there is strong potential."
The Opotiki mussel farm was understood to be close to harvesting on a commercial basis and the mussels were expected to be handled by North Island Mussels in Tauranga.
Meanwhile, a new mussel hatchery opened this month at the Cawthron Aquaculture Park
in Nelson. It is part of a SPATnz (Shellfish Production and Technology New Zealand Limited) Primary Growth Partnership with the Ministry for Primary Industries.
Mussel processing
North Island Mussels (NIML) is the North Island's only major mussel processing operation.
Predecessor company North Island Mussel Processors, founded in 2009 with the world's first automated mussel-opening machine, went into receivership in 2012 after problems with one of its shareholders.
The other two shareholders, Sanford and Sealord, became 50-50 owners in 2012 and set up NIML to run the business.