Aodhan Connolly said the Northern Ireland Protocol had produced the greatest disruption to commerce since the foundation of the state a century ago.
Northern Ireland remains part of the EU’s single market for goods.
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Supermarkets have been given a grace period until April where they do not need the certificates for most products and businesses, and British ministers want an extension.
Mr Connolly said: “It has to lead to certainty, not just for Northern Irish businesses but for those people who want to invest in Northern Ireland.”
The British Government is pressing the EU for an extension to grace periods on checks on supermarket goods in transit from the rest of the UK to Northern Ireland until 2023.
Mr Connolly represents companies like Lidl, Asda and Sainsbury’s and is director of the Northern Ireland Retail Consortium.
He said the opportunities arising from Northern Ireland’s place in the UK and the EU single market needed to be promoted more widely to European customers.
Mr Connolly told Stormont’s Economy Committee that being part of the EU and Northern Ireland presented opportunities for the manufacturing sector, but risked leaving others behind.
“We need to ensure that we take all sectors of business with us.
“There are going to be some changes.
“It is a new trading regime, it is the biggest economic shift as far as supply chains and how we trade since the foundation of the state 100 years ago.”
Unionist politicians in Northern Ireland are demanding the end of the protocol, claiming it has driven an economic wedge between the region and the rest of the UK, undermining the Union as a consequence.
The protocol was designed by the EU and UK to avoid a hard border on the island of Ireland.
It achieves this by moving regulatory and customs checks to the Irish Sea, with goods imported into Northern Ireland from the rest of the UK subject to a range of new processes.
Mr Connolly said an extension of grace periods was needed to ensure the stability of businesses.
“We need the certainty of a long-term workable solution, designed with businesses, not done to businesses.”
He said that had to be affordable and remove frictions to allow firms to be competitive.
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