Up to 200 trucks a day are being sent back from UK crossings to the EU because they lack the correct papers, officials have said.
Emma Churchill, the head of the border and log delivery group in the cabinet office, said between three and eight percent of trucks were turned away at ports.
This corresponds to between 100 and 200 vehicles per day.
When she presented evidence to the Commons Public Accounts Committee, she said the numbers were far lower than expected after the Brexit transition period ended on December 31.
She said roughly half of the time this was due to drivers not having a negative coronavirus test after the French introduced new controls late last year.
She said traffic at the canal ports was “completely free flowing” and most drivers arrived with proper documentation.
“That’s because the general willingness of dealers has been higher than we feared or expected,” she said.
“The number of setbacks on the Short Straits is around 5%, which is very, very much better than feared, but we have to watch this very, very carefully as the volume increases.”
However, the committee members accused officials of downplaying difficulties in moving goods from the rest of the UK to Northern Ireland after the introduction of controls under the provisions of the Brexit Take-Back Agreement.
Alex Chisholm, the permanent secretary in the cabinet office, said there was a shortage of “small” groceries on supermarket shelves.
“There haven’t been very many incidents. We solve the problems as soon as they occur. The extent of the problems is not significant,” he said.
However, Conservative MP Sir Bernard Jenkin said some operators had problems with the way the rules were applied.
“A truckload of potato chips was kept for two days because the haulier could not prove that the potatoes the chips were made from had not been imported into the UK from elsewhere. That is ridiculous,” he said.
Jim Harra, chief executive of HM Revenue and Customs, insisted that there was no need to prove their origin as the chips were intended for business in Northern Ireland and there was no risk of them entering the EU.
Officials also said the problems that caused delays for some seafood exporters to the EU after the end of the transition period have now also been resolved.
James Quinault, Head of the Europe Group at the Department for the Environment, Food and Rural Affairs, said: “In the early days there were problems, particularly with the customs transit system.
“These are problems with the EU system but we managed to resolve them quickly and provide guidance to the industry and these problems are now resolved.”