Thousands of delicatessens and other specialist food shops have said new border rules that come in from Wednesday are likely to mean reduced choice of products for consumers.

The Guild of Fine Food (GFF), which represents 12,000 businesses, has raised fears that European suppliers of specialist foods such as cheeses and meats will stop supplying the UK as a result of the additional red tape for imported goods.

John Farrand, the managing director at the GFF, said: “I’m just worried that we are going to end up buying and selling only mass produced products. Are we going to see the end of smaller, more interesting products, which are ultimately better for the planet?”

The government is introducing the biggest changes to the way the UK imports food and plant products from the EU since it left the single market in January 2021.

The changes, known as the Border Target Operating Model, will require all imports of medium and high risk products, which include meat and dairy and the majority of plants, to be sent with export health certificates from Wednesday.

On 30 April, these products will receive physical checks at the border before they can enter the UK.

The new requirements have caused widespread concern that they could result in some smaller suppliers giving up on supplying the UK because of the extra costs.

Farrand said while large supermarkets and large exporting businesses would have the financial base and resources to continue ensuring supply, smaller retailers and wholesalers would not.

Andrea Rasca, the CEO and founder of Mercato Metropolitano, which runs a number of sites in London hosting dozens of independent food outlets, agreed that the new rules would deter EU suppliers, and urged the government to rethink.

Rasca said: “For independent retailers, these new import rules could result in many specialty retailers or delis having empty shelves and at worst having to close down due to the limited supply of produce coming into the UK.”

According to the government, the additional costs of the border checks and new certification requirements could add up to another £330m a year of extra costs for business.

Nick Carlucci, the sales director at the Italian food importer Tenuta Marmorelle, said that he had heard of several suppliers in Italy opting against exporting to the UK because of the post-Brexit red tape.

He said: “They have said it is not worth our while – the UK is not a big enough market for us. It’s a shame because the end user will ultimately lose these specialist products.”

In a statement, the government said the new controls would help prevent the import of diseases and pests from overseas.

The biosecurity minister, Lord Douglas-Miller, said they were “proportionate and pragmatic” and the government had worked closely with industry before finalising plans.

He added: “The controls introduced today strike the right balance between trade and biosecurity.”

MPs, however, have raised concerns about whether biosecurity will be sufficiently protected.

In a letter to the environment minister, Steve Barclay, the environment, food and rural affairs committee said that it was particularly concerned with the plan to carry out border checks at the Sevington border post, which is 22 miles inland from the Port of Dover.

The letter said that the plan presented a “potentially serious biosecurity risk” and also compromised compliance regarding lorries carrying goods.

It added: “We understand that drivers will be under no obligation to go to Sevington, if asked to do so. As such, we have real and reasonable concerns about the geographic dislocation of the inland border facility from the point of entry.”

A government spokesperson said: “This is not something we expect to see, having developed the model and its timelines for implementation through extensive consultation with industry stakeholders.

“Our plan will help deliver the most advanced border in the world, progressively introducing an innovative approach to importing.

“This includes using technology and data to make it simple for businesses to trade, while maintaining the flow and security of goods helping to keep the UK safe, while protecting our food supply-chains and our agricultural sector from disease outbreaks that would cause significant economic harm.

“We have and will continue to work with industry, ports and airports to prepare for the changes being implemented.”