Beekeepers are concerned they may be lumped with the costs of cleaning up future biosecurity breaches that are not their fault.
Primary industry groups are currently looking at signing up to a deal with Government to work together on improving post-border biosecurity controls.
The Government Industry Agreement (GIA) would allow industries to help identify the biosecurity risks of greatest concern to them, and manage those risks through joint investment with the Government.
National Beekeepers Association co-chief executive Daniel Paul is worried the GIA would only give beekeepers a say in biosecurity systems post-border.
"Our industry would be far more comfortable if the agreement allowed us to have serious input into pre-border controls as well."
Beekeepers could well be left responsible paying for a biosecurity breach they had no opportunity to prevent, he said.
He cited the Government's intention to allow Australian honey into the country, which had the potential to bring in three new pests and diseases, Paul said.
"We don't have any concerns that consumers would stop buying New Zealand honey.
"What we are concerned about are the chances of a serious biosecurity breach if Australian honey is allowed in. Who's going to pay for that?"
The Government could not on the one hand allow a new product into the country and then expect the industry to pay the costs if something went wrong, he said.
The benefit of the GIA was that beekeepers would at least get to sit around the table and talk with the Ministry for Primary Industries (MPI), he said.
"There's sufficient benefit to warrant signing up. It would be foolish to write it off right now.
"If we're not a signatory and something happens, we just won't have the chance to talk with MPI about how to deal with it."
Paul said he hoped discussions now with the MPI would lead to a fair cost-sharing agreement.
MPI said the GIA, planned to start formally on July 1, 2013, would give primary industries a better say in biosecurity preparedness and response activities.
A Joint Working Group, made up of industry members and the MPI, was currently in discussions over what the agreement would look like and how the cost-sharing would work.
The working group was expected to produce a draft Deed of Agreement for industry bodies to comment on later this year, with industry members to eventually vote on whether to sign up.