Trade groups have warned that consumers could see a rise in food prices after the UK government announced the introduction of post-Brexit charges on imports of EU food and plant products later this month.

The government has published details of fees – known as the common user charge – which will apply to small imports of animal products and plants, such as sausages, cheese and yoghurt, entering the UK from the EU through the port of Dover and through Eurotunnel at Folkestone.

The Department for Environment, Food and Rural Affairs said the fees of up to £145, which come into force on 30 April, will pay for border inspections and improve biosecurity by preventing the import of plant and animal diseases into the UK. The charges apply to imports entering the UK and transits entering and leaving.

Trade groups criticised the charges and said the move would increase business costs and food prices and lead to potentially fewer choices for shoppers.

William Bain, the head of trade policy at the British Chambers of Commerce, called the move “extremely disappointing” and said the government had failed to listen to industry concerns.

“The level of import charges shows scant regard to the interests of both businesses and consumers,” he said. “A flat rate fee for bringing most animal and plant products into the UK is a hammer blow for small and medium-sized importers. It’s also deeply concerning for retailers, cafes and restaurants.”

He said importing a small consignment of goods with only five different meat, poultry, egg, milk or some fish products in the medium-risk category meant firms would face a bill of £145 a package under these proposals.

Phil Pluck, the chief executive of the Cold Chain Federation, which represents importers of perishable goods, said the charges had been introduced “at the last minute”, which he said gave companies very little time to alter their commercial arrangements with EU customers.

“This is in no way helpful to UK-based importers and the whole EU supply chain. It reinforces the government’s slapdash approach to a vital part of UK plc,” he said.

“Our main concern is that this is now certain to negatively affect food prices. The confirmation that common user charges will apply from 30 April means that UK importers of medium and high-risk goods will have to pass this cost on to either the EU importer, the smaller UK retailer, or the UK consumer.

“Ultimately, this will increase business costs and food prices and potentially lower choices for the shopper.”

James Barnes, the chair of the Horticultural Trades Association for the UK garden industry, said the announcement had come at the “11th hour ” and he feared the competitiveness of UK horticulture “will be again hit by a cost hike for no material gain”.

Barnes said 90% of the growers it represented imported plants at some stage of the growing cycle and almost all were small businesses, many of whom would be expected to pay the £145 maximum charge.

“This will be a huge new cost burden for many, hitting SMEs hard,” he said, adding the policy “feels like it is constructed on the back of an envelope at best”.

Barnes added: “The charges will undoubtedly increase costs, potentially reduce consumer choice, and increase the likelihood of empty shelves, thereby impacting biodiversity and meeting our nation’s environmental targets.”

The UK government has delayed the introduction of the charges five times since the UK left the EU, partly to give businesses time to prepare and to reduce disruption to supply chains.

The UK government said: “The charge is designed to recover the costs of operating our world-class border facilities where essential biosecurity checks will protect our food supply, farmers and environment against costly disease outbreaks entering the UK through the short straits.

“The charges follow extensive consultation with industry and a cap has been set specifically to help smaller businesses. We are committed to supporting businesses of all sizes and across all sectors as they adapt to new border checks and maintaining the smooth flow of imported goods.”