Marks & Spencer has warned that up to 15% of its food product lines could be unavailable in its Northern Ireland shops in January.
From 1 January, Northern Ireland will stay in the EU single market for goods but the rest of the UK will leave.
The EU has strict rules on which food products can enter its single market.
Negotiations between the UK and EU on how these rules should be applied on food entering Northern Ireland from Great Britain are ongoing.
This matter is separate from the trade talks between the EU and UK and will not be directly resolved by a trade deal.
At issue is the level of checks and bureaucracy and whether some products can be sold at all.
A piece of administration known as an Export Health Certificate (EHC) is central to the problem.
Products of animal origin - meat, milk, fish and eggs - need an EHC to enter the single market.
EHCs are an expensive piece of administration, signed off by a vet, which could add thousands of pounds of cost to of a typical supermarket shipment.
Retailers need 'urgent answers from government'
A further problem is that for some products deemed high risk by the EU, such as chilled mince or sausages, no EHCs are available.
That could mean those products could not be shipped from GB to NI but could be sourced locally or from within the EU.
Marks & Spencer told BBC's Good Morning Ulster programme that it was committed to Northern Ireland and wanted to provide the same range of products.
But it added: "To keep this promise, retailers need urgent answers from government on several aspects of the NI 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."
UK supermarkets and the government are pressing the EU to show maximum flexibility on this issue, but nothing has yet been agreed.
On Thursday NI Secretary Brandon Lewis told the BBC that negotiations on the issue have intensified and he appreciates that supermarkets urgently need an answer.
If there is disruption to NI food supplies in January, it is possible that the UK government could trigger the safeguards clause in the Brexit withdrawal deal.
It states that if applying the deal leads to '"serious economic, societal or environmental difficulties that are liable to persist or to diversion of trade" then appropriate safeguards measures can be taken.
These measures must be limited to what is "strictly necessary in order to remedy the situation".