FERA is reviewing the fees for statutory checks in England and Wales, which have been the same for more than 10 years in some cases. The current income from businesses is around 40 per cent on average and there are fears that the fee rise could deter exports to mainland Europe.
The eight-week consultation will gather feedback on the proposed changes and views on efficiencies to reduce costs in the future.
FERA director of policy and regulation Tony Harrington said: "We are currently reviewing all our regulatory activities, including what roles and responsibilities we and industry should have.
"We want to hear from as many stakeholders as possible about how we implement increases to the charging schemes. We also want ideas on what changes we could make over the next three years to regulatory work to minimise these increases."
Other consultations due to be announced over the next two months include export certification services, seed marketing regulations and UK national listing and plant breeders' rights.
Plants for Europe owner Graham Spencer said: "The feeling in the industry is that inspection fees have been low for some years. We are seeing more inspectors at Heathrow and Gatwick Airports as a result of more investment, and that is a good thing."
To contribute, see www.fera.defra.gov.uk/planthealthconsultation.