Environment Minister Edwin Poots has said the UK government is paying for work to expand post-Brexit control points at local ports, which could cost an estimated £40m.
Last week, Mr Poots indicated he wanted to pause the work on the food and animal control points.
However, he told Radio Ulster's Farming Matters that the "UK government have made it clear they want it to happen".
"They're paying for it to happen," he added.
It is believed Mr Poots wanted to pause the work in order to wait until the UK's talks with the EU became more clear.
His stance led to a row between Stormont ministers last Thursday night.
Carrying out the work on the facilities is seen as a crucial part of the preparations for the regulatory checks required in the UK and the EU's controversial Brexit protocol.
Stormont officials and other ministers argued that halting the project would be in violation of Stormont's international obligations.
Over the weekend, UK Environment Secretary George Eustice wrote to Mr Poots to clarify the kind of work which is required.
The minister told BBC News NI that the UK government is paying for the work and the position of the UK's environment secretary will be adopted.
Later on Tuesday, he told Farming Matters that it is still not known "what is actually required" at the control points.
"I wasn't ready to sign off £40m of public money on something where we didn't know what was required," he said.
"George Eustace has been prepared to do that, and he was prepared to say the following, in the view of Defra (Department for Environment, Food and Rural Affairs), is required.
"And it is Defra that will actually be paying for it."
In a statement from Northern Ireland's Department for Agriculture, Environment and Rural Affairs (DAERA) said: "There is a binding international agreement passed by Westminster to implement the Northern Ireland protocol.
"DAERA officials are working to implement points of entry in order to meet those requirements as set out by the Defra minister and the UK command paper, The UK's Approach to the Northern Ireland Protocol.
"Approved points of entry are a legal requirement for the purposes of protecting public health, securing safe food supply and protecting animal and plant health."