Federated Farmers says the primary sector should not have to pay for biosecurity incursions as is proposed under the Government's Biosecurity Law Reform Bill.
The bill is being considered by Parliament's Primary Production select committee.
Federated Farmers' biosecurity spokesperson John Hartnell says the bill is about transferring the cost of biosecurity to landowners and primary industries and lowering the priority given to border clearance.
The bill proposes some of the most significant changes to the biosecurity system in more than a decade.
They include developing government-industry agreements and sharing the costs with industry groups.
Mr Hartnell says the cost of biosecurity incursions should be put on importers, where the risk lies - not the export sector.
He says the Government is looking to charge different industry groups to fund biosecurity in the future and that would mean they would be expected to meet part or all of any costs involved.
Mr Hartnell says for example, the bee industry would be bankrupt if it were expected to cover half the cost of fighting the varroa bee mite.
Mr Hartnell says varroa is estimated to have cost between $14 million and $16 million.
Farmers and other industry members have enough compliance costs now without having to fund the biosecurity system, he says.
Biosecurity Minister David Carter says the primary sector will have to help pay for biosecurity incursions if they want a say on how they are managed.
Mr Carter rejects claims that pests are getting into the country because the Government has cut staff numbers.
Staff levels were adjusted to meet the amount of trade that was coming through the border, he says.