Border control posts at the north's ports will "almost certainly" not be ready in time due to a dispute over IT with the EU, Stormont minister Edwin Poots has said.
British environment secretary George Eustice has written to the devolved agriculture department pressing for action.
When the Brexit transition period ends on December 31, some checks will be needed on goods like animal products entering Northern Ireland from Great Britain.
That is because it will continue to follow the EU's regulatory rules after Brexit unless a wider trade deal is secured with the UK.
Mr Poots said: "One of the issues that is outstanding relates to IT.
"There seems to be a bit of an issue between an IT system used in the UK for many years and the EU's non-acceptance of that, which will almost certainly ensure that we are not operationally ready."
Mr Poots wanted to pause the work following the British government's legislative move to guarantee unfettered access throughout the UK's internal market.
On Tuesday, he told the assembly Mr Eustice had given a clear expectation to the senior civil servant in his department, who was taking it forward.
Mr Poots said: "I have no legal remit to stop it, in that all of the advice from the departmental solicitor's office, and indeed the advice from the attorney general, would indicate that a ministerial direction to an official that would oblige an official to break the law is not a direction that would have any standing."
The Northern Ireland Protocol, part of the Brexit divorce deal, will see the country continue to enforce the EU's customs rules and follow its rules on product standards.
It is designed as a fallback option should a deal not be reached with the EU and is intended to ensure the border remains free-flowing.
