Importers of food from the EU into Britain have said newly introduced post-Brexit checks could increase their costs by up to 60%, pushing up prices for customers and driving some shops out of business.

After five previous delays, the UK government on Tuesday introduced the physical checks on animal and plant products entering from the EU, having revealed at the start of this month that it would be implementing a common user charge (CUC) of up to £145 per consignment.

However, importers and haulage companies have criticised the lack of clarity over what was meant by a “consignment”, with many assuming that the cap applied per lorry. In fact, vehicles with a wide variety of products from different locations could be forced to pay many multiples of £145.

Haulage companies carrying meat and dairy products from Poland and other eastern European countries said the new charges mean they will now have to pay hundreds of pounds for each lorry, adding significant costs to operations.

While the government has scaled down the number of inspections to avoid disruption, meaning queues at the border did not materialise on Tuesday, most lorries bringing food and plants from the continent through Dover and the Channel tunnel still face having to pay the CUC.

One of the biggest importers of eastern European goods to the UK, sending more than 70 lorries every week and supplying 1,000 businesses, said the government needed to be clearer on what a consignment meant and to alert companies that they were facing costs much higher than £145.

The company, which preferred not be named, said some of its trucks would now have to pay £1,500 (€1,750) extra to cover the costs, an increase of about 60% on the €3,000 it usually costs to transport goods to the UK.

Adriana Zalewska, from the small importer Kin Global Distribution, said its lorries could often carry shipments with several types of meat, dairy and other fresh produce, with the new fees adding upwards of £1,300 a shipment.

She said: “This means that food prices in the UK will have to rise, as costs will be passed through the supply chains. We are concerned this will directly and immediately hit small businesses, such as shops, local distributors and import businesses, forcing them out of the market.”

Piotr Liczycki, the managing director of the Polish company Eljot Transport, which sends 2,000 lorries to the UK each year, said it was now expecting to pay between £300 and £2,000 more for each lorry, which could add between £1m and £1.5m to operational costs this year.

Businesses had already criticised the fact that details of the CUC were released by the government only at the start of April, just weeks before the checks were due to come in.

Under the rules, the £145 cap on checking fees applies for each consignment that has a common health entry document (Ched) attached. On a lorry with a mixed load of products from different suppliers, a Ched is required for each type of product – for example poultry. Sometimes extra Cheds are issued at different loading locations.

This means lorries with a wide variety of products from different locations, such as one carrying beef, milk and eggs, will be forced to pay multiples of £145.

The CUC is being levied on goods coming in through the Port of Dover and the Channel tunnel to cover the cost of checks and operations for the only government-run border control facility at Sevington, in Kent.

The post-Brexit checks also came in at other ports across the country on Tuesday, which have privately run border control posts that will set their own charges for importers.

While these checks are light-touch and focused on the highest-risk products, the government has promised to scale them up in a “sensible and controlled way”.

Michael Szydlo, the co-founder and chief executive of the food industry customs agency Quick Declare, said that in some cases loads had incurred CUC fees of £3,000.

He has written to the Department for Environment, Food and Rural Affairs urging it to reduce the costs for imports, arguing they could cause permanent damage to food supply chains.

A government spokesperson said: “These border checks are fundamental to protecting the UK’s food supply chain, farmers and natural environment against costly diseases reaching our shores.

“Their cost is negligible compared to the impact of a major disease outbreak, such as foot and mouth disease in 2001, which cost businesses and our wider economy more than £12.8bn in 2022 prices.

“We will continue to work with and support businesses throughout this process to maintain the smooth flow of imported goods.”