Fire and Emergency assistant area commander Mark Tinworth said the fire was "fully involved" when crews arrived.
He said the industrial building had been "severely affected" by the fire, which destroyed honey, packing material and machinery.
Firefighters contained the fire to the building and would work through Thursday and possibly Friday dampening hotspots.
"There could be hotspots underneath corrugated iron and to get to that you have to lift the iron off," Tinworth said.
"We're probably going to have to work with machinery to access all the hotspots."
The sun rises on the destroyed Bees' Inn Apiaries at Ohaupo. Photo / Bethany RolstonDuring the battle to bring the blaze under control, access to West Rd from SH3 was closed, with detours through Kaipaki Rd.
Waikato Regional Council staff were also at the scene and helped contain the run-off from seeping into waterways.