The UK government has submitted applications to the EU to create Border Control Posts (BCPs) at Northern Ireland's ports.
BCPs are facilities used to check animals and food arriving in the EU single market.
At the end of the Brexit transition on 1 January, Northern Ireland will stay in the EU single market for goods.
The rest of the UK will not, so some products entering NI from GB will need to be checked at the posts.
A UK government spokesperson said: 'We have always been clear that, following the Northern Ireland Protocol, there would be a limited expansion of facilities at some existing entry points, where certain controls for animal and plant health already take place.
'We have submitted applications for these entry points on time and there will be no new customs infrastructure in Northern Ireland.'
Last week, Northern Ireland Agriculture Minister Edwin Poots wrote to his counterpart in Westminster saying that he was not cooperating with a full application until he got more clarity on how BCPs would be used.
In a letter to DEFRA Secretary George Eustice, Mr Poots acknowledged there is a legal responsibility to create the BCPs.
However, he added: "I am currently unable to present a full application due to the lack of certainty around a number of key areas including the level of checks required."
Mr Poots then posed a series of questions such as whether major supermarkets could be exempt from checks as "trusted traders" and whether a check of 1% of non-trusted trader goods would be acceptable.
However DEFRA has proceeded with the application.
It is able to do this because engagement with the EU via the UK Government - as international relations - are not a devolved matter.
The UK spokesman added: 'We are continuing to work closely with the executive on proposals to minimise requirements on the movement of food and agricultural products, in line with the approach we set out in our May command paper.'