The end of the Brexit transition period has forced a “difficult adjustment” on retailers in Northern Ireland, the industry said.
Northern Ireland Secretary Brandon Lewis maintained that empty supermarket shelves in Belfast this month were due to the UK variant of coronavirus, which saw Europe close its English Channel ports before Christmas.
The senior Cabinet member has argued that there is no Irish Sea border created by the Protocol and the shortages have nothing to do with the special EU divorce deal.
Retail NI chief executive Glyn Roberts said: “The big takeaway for the Secretary of State and the UK Government is making sure that Great Britain suppliers who supply into Northern Ireland do make sure that they comply with the paperwork and make sure they are aware that how they trade with Northern Ireland has changed.
“There was certainly a knock on effect – the reality is that this new regime we have in relation to trade between Great Britain and Northern Ireland certainly has been a very difficult adjustment.”
The protocol means Northern Ireland follows the EU’s rules on matters like animal product standards to avoid a hard Irish border on the island.
Traders have faced a “challenging” period but are adapting to extra red tape created by the protocol, Mr Roberts added.
They are also attempting to source more products locally.
He represents independent small and medium-sized firms, not large supermarket chains.
He said: “We are confident we will get through it.
“Members have taken a very solution-based approach and independent retailers are probably, out of all the sectors – we are probably the most adaptable to change.
“I would be optimistic that it will, to use a Northern Irish expression, collapse into place.”
Some supermarket shelves were depleted this month as suppliers grappled with new rules surrounding sending goods from the rest of the UK to Northern Ireland.
The Secretary of State told BBC Radio 4’s Today programme: “That’s actually something we’ve seen across other parts of the UK as well, nothing to do with leaving the EU, nothing to do with the Northern Irish protocol but actually to do with some of the challenges we saw with Covid at the Port of Dover just before Christmas and the impact that had on supply lines coming through.
“I have to say supermarket supply lines at the moment are in good fettle.”
Hauliers’ representatives in Northern Ireland have also suggested the problems are being resolved.
Mr Lewis said there was no reason for lorries to return empty from Great Britain due to excessive paperwork.
Smaller food traders have struggled to adapt to problems with multiple consignments travelling in one lorry, meaning loads have to be resealed and certified by officials several times.
Mr Lewis said: “Even on foodstuffs, there’s no reason for that to be the case.”
A soft-touch three-month period has been negotiated with the EU for regulating supermarket goods transported from the rest of the UK.
Mr Lewis said the UK is working with the EU to get a “permanent resolution” before that ends.
The Democratic Unionist Party has strongly criticised the new arrangements.