It is estimated between 5000 and 6000 beehives were washed away or damaged in Hawke's Bay and Tai Rāwhiti during Cyclone Gabrielle.
Apiculture New Zealand chief executive Karin Koss said it has been working to quantify the extent of the damage but it was clear there has been significant destruction.
"We're still working with beekeepers to get a sense of the damage but our early estimates at this stage is that between 5000 and 6000 hives have been lost or damaged in the flooding.
"But there's probably at least the same amount if not more hives cut off from road access, so people can't get them to see if they're okay."
Koss said that was concerning as keepers could not monitor bee health and treat hives for diseases like varroa mite and American foulbrood disease.
She said it was to early to say what financial impact the cyclone would have on the industry.
"Some companies insure hives but I suspect many don't. It's already been a tough summer with honey production way down so this is just another blow for beekeepers and the industry this year."
Hawke's Bay Bee Club represents about 80 hobbyist beekeepers in the region.
President Graham Heaven lost 100 of his 120 hives.
"They were mostly on the flats in orchards so I knew it would be bad before I even went to check on them, but it was worse. Most of them were completely washed away.
"Some beekeepers have lost everything, lots of hives were full of silt so they either need to be cleaned out or thrown out.
"I know dozens of hives have washed up on the shore but there's so much debris it's too hard to get to them."
Heaven said because the flooding happened at night the bees would have been inside their hives so likely did not survive.
"That's going to have massive flow-on effects in spring because there won't be enough bees to pollinate all the crops in Hawke's Bay like the kiwifruit and apples."
Arataki Honey which has 10,000 hives in the region estimated it has lost 400 hives.
Company director Rhys Flack said their main problem at the moment was accessing hives to check on them.
"We have guys that just to get south of Wairoa have to go through to Ōpōtiki down through Gisborne so that's a four-day trip instead of a one-day trip, but what we're finding is that lots of the hives need feeding and treatments to get rid of varroa mite before winter.
"But we're very fortunate and I know other beekeeping businesses that were on lower land have had it far worse, so we're counting our lucky stars we still have an operating business."
Flack said with little honey being collected due to bad summer conditions alongside the damage meant the business has a lot of additional costs and no revenue.
"It will go down as one of the worst in the company's 80-year history."
RNZ
