Supermarkets in Northern Ireland are struggling to fill their shelves because of the new post-Brexit trading arrangements, with hundreds of products caught up in supply-chain delays.

Marks and Spencer, Sainsbury and Tesco have all been hit with new red tape and customs paperwork introduced following the end of the Brexit transition period on January 1.

The new rules are part of the Northern Ireland protocol — the mechanism agreed by the UK and EU in 2019 to avoid a hard border on the island of Ireland.

Under the protocol, Northern Ireland continues to apply EU internal market and customs rules to maintain frictionless trade over the land border with the republic. This means vast volumes of new paperwork are required to process Irish Sea checks on shipments from Great Britain to the region.

The extra red tape has left many food suppliers facing lengthy delays on shipping goods to the region, resulting in empty shelves for time-sensitive products like fresh fruit and vegetables and chilled meat.

Glyn Roberts, chief of Retail NI, an industry group in the region that represents 1,800 independent retailers and wholesalers, said a “huge amount of Brexit bureaucracy” had caused considerable supply chain problems for Northern Ireland's retailers.

“I think at the end of the day it will collapse into place but these next few months are going to be critical,” he said. “Ultimately this is not the wonderful land of milk and honey promised by the people who campaigned for Brexit but we’ve got to make the best out of a bad situation.”

The problems have led to criticism of Boris Johnson’s government from the pro-Brexit Democratic Unionists, who opposed the protocol because they wanted Northern Ireland to leave the EU on exactly the same terms as the rest of the UK.

Sammy Wilson, DUP MP and the party’s Brexit spokesman, said that “supermarket shelves are empty” in Northern Ireland.

In the House of Commons on Monday he urged chancellor Rishi Sunak to get a grip on the situation. But Mr Sunak said: “I know goods in aggregate are continuing to move smoothly between Great Britain and Northern Ireland.” Ministers would work to address individual problems, the chancellor added.

M&S has had to pull roughly 5 per cent of its range from shelves in Northern Ireland temporarily to minimise risks of lorries becoming stuck due to missing paperwork. The retailer said it was looking at options to source more products locally.

Sainsbury has adopted the unusual practice of stocking some locally sourced Spar-branded food in its Northern Ireland stores in a bid to maintain continuity of supply. The chain said “a small number” of products were temporarily unavailable in Northern Ireland “while border arrangements are confirmed”.

Henderson, owner of the Spar franchise in the region, said it was supplying “a range of fresh and frozen goods” under the arrangement. The wholesaler said it had built up stocks over the past three months to mitigate the impact of Brexit.

Tesco said: “We have a good supply of products coming into Northern Ireland. There has been a short delay on certain products but we’re working with suppliers to get these back on the shelves as quickly as possible and direct customers to alternatives where we can.”

Aodhán Connolly, director of the Northern Ireland Retail Consortium, which represents large supermarket chains, said “all retailers” were under pressure to a greater or lesser extent as the new system bedded down.

But he added: “To put that into perspective there are a few hundred items that are not available at the moment, when a large supermarket has over 40,000 items.”