Northern Ireland potato firms will not be able to export to the EU in the event of a no-deal Brexit.
Hundreds of tonnes of table potatoes and bulk shipments of chips are sent to the Republic of Ireland every week.
But government guidance says trade to EU countries will face restrictions in the absence of an agreement.
One of NI’s biggest processors Wilson’s Country said it had lorries crossing the border six days a week to supply southern supermarkets.
Managing Director Lewis Cunningham said hundreds of fast-food outlets in the Republic of Ireland, which rely on chipped potatoes from Northern Ireland and Great Britain, could also face supply problems.
Mr Cunningham said he remained optimistic a resolution could be found but the firm had a contingency, which he declined to disclose.
The European Union has said that after Brexit, UK potatoes will not be eligible to be marketed because of plant health regulations.
And it has refused to consider a UK application for its certification process to be granted equivalence, which would have allowed existing trade to continue.
The EU said it would not consider the application until the withdrawal negotiations had been concluded.
The government says it is aware of the implications of the ban for businesses and it will resubmit the certification application immediately after negotiations are concluded.
The government guidance makes it clear that EU certified potatoes will, for the most part, continue to be accepted in the UK, without major restriction.