Customs agents and businesses have complained to the UK government that they have been charged for checks on goods that never took place, after post-Brexit controls on food and plant imports from the EU were imposed on British importers.

In an online meeting on Tuesday with officials from the Department for Environment, Food and Rural Affairs (Defra), dozens of disgruntled agents highlighted errors with the new system that one called “chaotic”.

In one case, a consignment could not be unloaded at a government-run border inspection facility at Sevington in Kent because of a design flaw in the inspection bay — yet the shipment owner was still charged for the inspection — the officials were told in the meeting.

Others said they paid for physical checks only to have their shipments cleared by a computer system, according to two people who dialled into the meeting.

From April a new charge was levied on anyone importing food or plants through Dover and the Eurotunnel in Folkestone, in order to recoup the costs of running the government’s Sevington border control post which inspects the imports.

Trade groups report that bills for the “Common User Charge” have already run into tens of thousands of pounds for some smaller businesses.

The added costs have prompted calls on the UK’s new Labour government to expedite a “veterinary deal” with Brussels that could reduce or remove the need for inspections and paperwork on most plant and animal exports. Talks are currently due to begin next year.

William Bain, the head of trade policy at the British Chambers of Commerce, said a deal was essential to prevent higher costs being passed on to consumers through higher prices.

“We would urge the government to work with business to find ways to mitigate this impact,” he added.

During this week’s online meeting, Steve Habbershaw, a customs agent in Dover, asked why he had been charged when most of his consignments had been automatically cleared without checks.

“The border situation at Sevington currently is rather chaotic,” he told officials, before asking whether revenue from the charge will “be spent to improve this”.

Additionally, a contingency feature that clears goods after two hours to avoid queues at ports left many businesses frustrated that they paid for checks that never took place.

Trade groups have warned of higher food prices and squeezed margins for importers as a result of the charges on all agrifoods consignments entering through Dover and the Eurotunnel. The charges were introduced on April 30, with the first payments taken last month.

One UK business, HunPro, a speciality importer of Hungarian foods, told the Financial Times it had to increase its staffing by 20 per cent just to deal with the paperwork from the new checks.

The company, which employs 20 people, took on four more people and said it had incurred a total of £8,000 in extra charges since the border was introduced.

“It’s just a huge extra expense for nothing,” said managing director Fulop Illes.

Richard Catt, of the Freight Liaison Group, said that pressure of the additional charges on small businesses was “difficult to swallow”, particularly given that the government was only carrying out the lowest possible number of checks on goods.

Sally Cullimore, policy director of the Horticultural Trades Association, which represents the UK’s plant nursery industry, said one small business member had received a bill for £27,000 for the first three months of border checks.

“That represents around 7 per cent of this company’s profits, which is significant when you consider this is an entirely new cost that delivers little or no benefit to the business,” she said.

The new post-Brexit border checks were introduced last April by the previous Conservative government after five separate delays. The government has estimated the new border would cost £330mn a year, but some industry estimates have put the total cost as high as £2bn.

At the time of the launch, the government said it had capped the costs at a maximum of £145 per consignment, but the industry warned that charges would quickly multiply for businesses such as plant nurseries and delicatessens that import multiple product types in a single lorry load.

“For our sector bringing in lots of small plants in small consignments you hit the cap of £145 for even a small trolley of plants,” said Cullimore. She added that a 30 day deadline to pay — despite the government invoicing after 90 days — was affecting the cash flows of businesses.

Susann Schmieder, the importer at German Deli, which has brought German food products to the UK for the past 20 years, said its bill had come to £550, but only because “our supplier in Germany is still unable to provide us with our range of products”.

She added: “The main issue is the paperwork, which means we couldn’t import as much as we wanted.”

Defra said the government was committed to seeking a veterinary agreement that would prevent “unnecessary border checks, get our great food exports moving again and tackle the cost of food”.

However, in the meantime it would continue to levy the Common User Charge in order to pay the operating costs of the inspections post at Sevington and “protect our biosecurity”, it added.

However, Peter Hardwick, trade policy adviser for the British Meat Processors Association, said Sevington also raises a Port Health Authority charge on all medium and high-risk goods that are, overwhelmingly, never sent for physical inspection, something that “really takes the biscuit”.