Yet, with the industry still three quarters of the way through honey collection, the full impact of the weather may not be known until as late as April.
Kos said it was unclear what this would mean for honey consumers.
"I think it is a bit soon to say, but, as there were good volumes of honey produced last year, I'm confident there won't be shortages for New Zealand consumers."
Plant and Food Research pollination scientist Dr David Pattemore said the manuka honey sector had been particularly hard hit.
"Nectar flow seems to have been low or non-existent in manuka."
This week, major manuka honey exporter Comvita warned of a 60 per cent shortfall in harvest expectations this season, with just 380 tonnes out of an average annual harvest of 974 tonnes now anticipated.
The slump meant its projected after-tax earnings had been revised from $17.1m to between $5m and $7m.
Comvita had been actively buying honey from third-party suppliers over the past 18 months so that customer demand could be met for at least the next year.
Pattemore expected many newcomers to the booming manuka honey industry would be hurting.
"People will have got into positions where they've taken out loans to purchase beekeeping equipment - so this will be a new situation for them to face."
Beekeeper Edoardo Canal, who has 400 hives on Kawau Island in the Hauraki Gulf, said the kanuka flowering season had lasted just days.
"We were hoping to get 50kg a hive minimum and now we've got zero, so I have to go back to work," he said.
"With the cold, southwesterly winds across the country, there's no one we know who's actually doing well."
But Pattemore said he hadn't received reports about pollination being affected in a similar way.
"Some plant species will do well in conditions that don't favour others," he said.
"Kiwifruit flowers, for example, don't produce nectar, so pollination of kiwifruit flowers won't have been affected in the same way."
Meanwhile, Pattemore had noticed a much lower rate of nest establishment at a bumblebee pollination trial his group has been running, confirming indications that queen numbers in spring were much lower than normal.
"But we've also received some fascinating reports of very large areas of active native bee nests.
"It has been an unusual spring and summer, which affects different plants and pollinators in different ways."