MARKS & Spencer has warned that up to 15 per cent of its food products may not be available in Northern Ireland stores in the new year.
From January 1, Northern Ireland will stay in the EU single market for goods but the rest of the UK will leave.
Regardless of whether a free trade deal is agreed, the Northern Ireland protocol will kick in at 11pm on December 31 and fresh food coming to the north from Britain will be subjected to checks including customs declarations.
The EU and UK are still negotiating a trade deal, although this will not solve issues around health certification checks on goods.
Products deemed high risk by the EU, including chilled mince and sausages, may be affected.
The chief executive of Sainsbury's, Simon Roberts, has already said that supply of many products to its Northern Ireland stores, including mince and sausages, as well as fish and dairy items, could be hit.
Marks & Spencer said retailers need clarity on aspects of the Northern Ireland Protocol, particularly on certification processes and labelling.
"Whist we have extensive contingency plans in place, if clarity is not given soon there is a risk to supply from the UK mainland, which could limit customer choice in Northern Ireland," it told the BBC.