Freight industry chief Seamus Leheny said confusion around new checks, including 'pre-notification' obligations imposed on inbound lorries from the UK was a result of what he said had been a rushed separation deal between the UK Government and the EU.
Mr Leheny, policy manager for Northern Ireland at Logistics UK, warned hauliers that failure to notify ports of their arrival would lead to delays and in some cases vehicles being turned away.
But he told Business Telegraph that there was some short-term leniency as companies come to grips with the new process.
One lorry driver, who did not want to be named said: "It's not a great day so far with teething problems but still very much in the middle of it."
The Antrim-based driver said five of his company's loads at one port in Great Britain had been postponed before noon.
Mr Leheny said as volumes increase in coming weeks and leniency wears thin, hauliers could face bigger problems without the right documentation and notifications. "This is affecting everyone," he added. "But you can't blame the businesses. A lot were not aware of what they had to do."
He said that food wastage and delays to get foods to their final destinations could be a worst case scenario if there were holdups at ports.
But NI grocers have said they are well prepared. Lidl said: "We are confident that our customers will be able to continue to shop all of their trusted Lidl products in our stores across the region." Meanwhile, Henderson Group, the name behind Spar, Vivo and EuroSpar, added: "We will continue to monitor the situation and implement contingency plans to try and ensure minimal disruption in supplies for our retailers and shoppers."
And Musgrave, which runs Centra, Mace and SuperValu stores, said it had been plannning extensively to minimise disruption including "increasing the amount of product held in NI and developing new delivery routes to avoid the UK landbridge for European-sourced goods".