The DUP has ordered officials to stop construction of permanent facilities for post-Brexit checks on agri-food goods arriving from Great Britain.
Northern Ireland agriculture minister Gordon Lyons also ordered a halt of further recruitment of inspection staff and an end to charges levied at the ports on traders.
Mr Lyons said the move was in response to the “practical difficulties’’ caused by the Northern Ireland Protocol.
Irish Sea trade checks, which are taking place at existing repurposed port buildings and other temporary facilities, will continue. Mr Lyons' decision relates to ongoing work on new purpose-built inspection facilities.
The minister made the announcement in an interview with PA news agency, citing uncertainty over the movement of goods when grace periods currently limiting protocol bureaucracy end at the start of April.
He told PA: "We don't know what the movement of retail goods from Great Britain into Northern Ireland is going to look like, we don't have the support in place through the digital assistance scheme yet either, and all of the SPS [sanitary and phytosanitary] issues around the end of the grace period are just so uncertain and it's a real nightmare for us and it's going to be causing us an awful lot of problems."
Mr Lyons said his officials have been warning him that the port control posts are unlikely to cope when the grace period ends and that supply chains were unlikely to hold up.
“The risk to Northern food supply in those circumstances will remain high so there’s a lot of practical difficulties with all of this and that’s causing us a huge amount of uncertainty,” he said.
The facilities were being constructed by the Department of Agriculture, Environment and Rural Affairs to fulfil a legal duty under the terms of the Northern Ireland protocol agreed between the UK government and the EU.
It comes amid a row about the implementation of the UK’s Brexit deal with the EU, which necessitates checks on goods entering the province from Great BRitain.
Red-tape restrictions on the movement of goods into Northern Ireland have mounted despite previous assurances from Westminster that such trade barriers would not exist.
The DUP claims the Northern Ireland protocol has put the union at risk.
Earlier this week, Arlene Foster and other members of her party launched court action to argue that the new goods checks were imposed without public consent.
Mr Lyons the UK and EU had to find “permanent solutions” to the issues caused by the protocol, adding: “We need that certainty.”