A group representing 30 major business bodies said the new requirement to notify the British authorities a day before European goods are sent would lead to big delays.
The SPS Certification Working group warned shelf life of fresh food could be cut by one fifth – while some produce could be unsellable.
The UK trade chiefs said the new demand was “unfeasible” and would push some smaller EU firms to end their relationship with British importers.
“A one-day delay to exportation can mean a 20% loss of shelf life, ultimately rendering the food unsaleable,” they said in a letter to environment secretary Steve Barclay.
The letter by the working group said the new paperwork imposed on EU companies before sending goods to the UK was “unfeasible for just-in-time supply to GB of perishable short-shelf-life fresh foods”.
Costly new health certificates are required for medium-risk food, animal and plant imports – including meat and dairy – from 31 January. And a brand new system for physical checks at the border comes into force on 30 April.
From next week, EU firms will need to pay for veterinary health certification – a new check within their own country – as well as fill out online paperwork to notify the UK the goods are coming.
And from April, there will also be extra costs to get through the inspection checks at the UK border. Business groups say some suppliers of specialist products – like French cheeses and Italian meats – will give up on Britain because of the extra expense and “huge hassle” involved.
The SPS Certification Working group – which includes the Chilled Food Association, the Fresh Produce Consortium and Dairy UK – warned that the new controls also limited the ability of EU food firms to send different products in the same trucks.
In the letter to Mr Barclay, the top business groups warned that it could “curtail imports, increase food inflation and reduce UK food security”.
EU food firms do not currently have to notify the UK authorities before sending meat and dairy products, so goods can get to Britain within hours of being packed up at farms.
Peter Hardwick, the British Meat Processors Association’s trade policy adviser, described the 24-hour period of pre-notification as “totally impractical”.
The expert told The Guardian: “Currently, if a vehicle is loaded in Ireland, it would expect to arrive at a border within six hours, eight at the most. The 24-hour rule would mean refrigerated lorries sitting in a park somewhere as the shelf life is affected.”
Business leaders are also worried at the lack of details about the opening hours of border posts, despite onerous physical checks coming in for high-risk and medium risk goods coming in April.
The Fresh Produce Consortium is angry that the government last week decided to class fruit and vegetables as “medium risk” – along with meat and dairy products – warning the costly checks would push up prices to consumers.
A spokesperson for the government said it was still committed to delivering “the most advanced border in the world”, arguing the new controls would protect the UK from “potentially harmful pests and diseases”.
They added: “We worked extensively with traders to ensure the new controls and requirements are clear and not burdensome – which is why low risk products face no additional certification or checks, while medium risk products will undergo reduced checks, minimising the risk of delays.
“We will continue to work closely with businesses across the UK as the controls are implemented.”