Lorries are unable to get into the UK, and the government is being urged to come up with a resolution as a matter of urgency.
Jon Swallow, a logistics boss with experience of nearly 40 years in the industry, said one of his HGVs had been sat at France's Dunkirk Port for three days due to issues with the Goods Vehicles Movement System (GVMS). Imports from the European Union now need to be processed using the GVMS.
The system, which HMRC implemented on 1 January, is one of the new changes regarding imports from the EU, with physical inspections not beginning until 1 July.
Lorry drivers have to upload information about the goods they are importing into the UK from the bloc, so they can get a barcode allowing them to cross the border.
Multiple companies declared that drivers are being denied permission to make the trip after having their reference codes rejected by the system, or having struggled to upload their information.
A spokesperson for HMRC, which handles post-Brexit administration at the border, said it was "aware of a small amount of user error issues with some of the new customs processes as traders and hauliers adjust to the new controls, which we expected and are addressing".
Swallow, who runs global logistics firm Jordon Freight, said it was not simply a case of "user error" "” i.e traders not using the new system correctly "” because government officials themselves had been unable to explain what's gone wrong.
"The delay isn't the most frustrating thing. The frustration is that is nobody can tell us what the problem is," Swallow told PoliticsHome on Wednesday morning. "We are asking technical questions, which at the moment they don't have the answer to."
Swallow, whose company specialises in European logistics, said he couldn't get assistance on the HMRC website, and didn't get the information he needed from HMRC's customs helpline.
"We've done everything at our end but the problem has been unknown for a day and a half, and that's hundreds to thousands in lost earnings," he said.
Angelos Panayiotou, who runs Windfall Logistics, told Bloomberg on Tuesday that he received an error message from the GVMS which meant a shipment of iced tea headed for the UK was stuck in the EU, despite having uploaded the correct information.
"There's no-one to go to help," he told the publication. "You've just got drivers stuck at port, unable to move."Industry representatives are trusting that GVMS issues will be resolved by officials in the next few days.
Jenny Chapman, Labour's Shadow Cabinet Office Minister in the House of Lords, said the difficulties encountered by businesses trying to get goods into the UK was "yet another illustration of poor planning and incompetence by the Conservatives".
She told PoliticsHome: "The government thinks that all it has to do is say the words 'Get Brexit Done' "” but it has no plan to make Brexit work. Labour would be working closely with our industries to tackle these challenges as we shape a new future outside of the EU."
The industry is not confident that it will receive a clear image of how new paperwork is affecting cross-border flow until later this month, as trade volumes in the first week of the calendar year are lower than normal and difficult to draw conclusions from.
However, there have been warnings that the additional cost and complexity associated with imports to the UK will force some European businesses deciding to ditch the market altogether, which will impact the British supermarkets.
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