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Depleted shelves in a Sainsbury's supermarket, in Belfast, on Jan. 11, 2021.

David Young/The Associated Press

When Britain cut its last ties to the European Union on Jan. 1, there were fears about border hassles, trade disruptions and long lines of trucks at the Port of Dover. Many of those fears have been realized, but not in the way most people expected.

Instead of problems moving goods between Britain and the EU, the biggest headaches have been felt shipping products from Britain to Northern Ireland. The situation has gotten so serious that supermarket shelves across much of Northern Ireland have been depleted and truckers have complained about delays of up to 12 hours at ports in Belfast and Larne.

On Tuesday, the chief executives of major grocery stores, including Tesco, Sainsbury’s, Asda, Iceland, Co-op and Marks & Spencer, called for the government’s “urgent intervention to prevent significant disruption to food supplies in the coming months.”

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The issue stems from a side agreement struck during the Brexit process that maintains the open border between Northern Ireland and Ireland, which is an EU-member state. The protocol effectively keeps Northern Ireland tied to EU regulations. That means that goods shipped into Northern Ireland from the rest of Britain must be checked to ensure they conform to EU standards.

The protocol went into effect on Jan. 1 along with a trade and co-operation agreement that Britain and the EU announced on Christmas Eve. A committee of British and EU officials has been working out the details about how the checks at the Northern Ireland border will be carried out. But many businesses say the process has been cumbersome and confusing.

“We have already seen that some suppliers, either because they do not understand the new regime or because it is too much hassle, have opted out of servicing the Northern Ireland market,” Aodhan Connolly, director of the Northern Ireland Retail Consortium, told a parliamentary committee last week.

“The supply chain will always take the path of least resistance, so quite frankly if it is too much hassle or if there is new cost to it, then Northern Ireland will get cut out of that supply chain and it is to the detriment of the Northern Ireland consumer.”

Some online retailers, including Amazon, have told customers in Northern Ireland that the red tape will limit the availability of some products and several grocery-store chains have cut back on shipping supplies from Britain. The shortages could get worse when a grace period ends in March and more regulations come into force.

Seamus Leheny, policy manager for Northern Ireland at Logistics UK, which represents the freight industry, said truckers had been assured the paperwork could be processed in 30 seconds. “I have had one operator tell me it has taken 12 hours for a declaration to be processed,” he told the parliamentary committee. “One large manufacturer in [Britain] had 15 lorryloads of food to go to Northern Ireland this week. Not a single one of them could move, because when the lorries arrived there was no customs declaration.”

Truckers who have mixed loads, made up of goods from several customers, face particular delays. Each batch of goods requires a separate customs form and “it is taking between 20 and 30 minutes per declaration just to do the admin work,” Mr. Leheny said.

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Farmers have also expressed fears about moving animals from Northern Ireland to England or Scotland. Under the protocol, if a farmer in Northern Ireland sends sheep or cattle to a livestock auction in England, any unsold animals can’t be returned for six months.

Ireland and Northern Ireland also have a highly integrated industry for processing agricultural goods, which could be affected by the protocol. Northern Ireland only follows EU regulations as per the protocol so the Irish border can remain barrier-free. But because Northern Ireland isn’t an EU member, the bloc’s trade deals with other countries could force the exclusion of Irish agricultural products that contain content from Northern Ireland.

Victor Chestnutt, president of the Ulster Farmers Union, said nearly half of Northern Ireland lambs are in Ireland and the finished products are sold around the world through EU trade deals. “We would be concerned about any resistance to parts of our lamb going out because they were produced in Northern Ireland,” he told the committee.

Prime Minister Boris Johnson called the issues “teething problems” and said the government was committed to working with businesses to find a resolution. “I don’t doubt that there will be problems,” Mr. Johnson told the House of Commons’ liaison committee on Wednesday. “Businesses must prepare for change. Things will be different and you have to get the right forms, you have to be conscious of the certificates that you need. But I believe that all that can be readily done.”

He added that if the issues became insurmountable, Britain could invoke a section of the protocol that allows either side to unilaterally impose safeguard measures. However, he said that would be a last resort.

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