Honey output plummeted to less than two thirds of the ten year average for the season to the end of June last year, according to a new report.
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The report by the Ministry for Primary Industries said bad weather was the reason.
It showed honey production was 14,855 tonnes, which was the lowest crop since the 2011/12 season.
However, in 2011-12, there were 47 percent fewer hives.
The reduced production has also hit farmers' incomes.
Apiculture New Zealand chief executive Karin Kos said the figures showed how difficult things have been for beekeepers.
"It was one of the most challenging seasons beekeepers have experienced in the last five years, and as a result we have seen lower volumes of honey," she said.
Ms Kos said climatic conditions affected North Island beekeepers more than those in the South Island.
And this diminished earnings for growers as prices for bee products and pollination services remained similar to the year before.
One bright spot was the export market, where earnings increased by 5 percent, despite the drop in volume.
China was the largest market, accounting for 25 percent of total honey exports by volume.
These figures refer to the year which ended last June.
For the current season, New Zealand has been wracked with two serious storms since January alone.
Despite that, Ms Kos argued output for the current production year might not suffer too much.
"We will definitely have a better season this year," she said.
"It started off quite strongly, the last couple of months have not been so great with the weather, but we looking at an average to slightly below average 2017 - 2018 season."
Meanwhile, the MPI report said the main issues for the industry continued to be the health of bees, competition for apiary sites, the theft of hives and attracting and retaining staff.
There was also some concern about the spread and potential impact of myrtle rust disease on mānuka plants, and uncertainty about what impacts this could have on mānuka honey production.