Declan Kearney said the plans, in a paper from DUP minister Edwin Poots, would place the Executive outside of the law.
But DUP junior minister Gary Middleton told the Executive Office Committee at Stormont that concerns had been raised about the legality of the Northern Ireland Protocol checks.
The prospect of Mr Poots attempting to halt the checks required under the protocol has emerged after he conceded a recent legal challenge on the issue.
A group called Unionist Voice Policy Studies had threatened to judicially review Mr Poots after claiming the ongoing port checks on goods arriving from GB are unlawful because they have not received the wider approval of the Stormont Executive.
Under Stormont rules, ministerial decisions deemed “significant” should be referred to the collective administration.
Conceding the legal challenge before it materialised into a judicial review, Mr Poots has stated an intent to bring a paper to the Executive asking for approval to continue the checks.
Such a move would raise the potential for the DUP to wield a veto to deny authority for the checks. However, the matter is unlikely to ever reach the Executive for debate, as Sinn Fein is set to use its veto to block it getting on the agenda.
If Sinn Fein does prevent the issue reaching the Executive, Mr Poots has signalled an intent to order a halt to the checks, contending that he would not have the legal authority to continue them.
Junior ministers Mr Kearney and Mr Middleton were questioned about the row during an appearance before their scrutiny committee.
Committee chairwoman Sinead McLaughlin said: “We are hearing reports that the agriculture minister intends to bring the implementation of the protocol to the Executive.
“Surely this is a matter of implementing the UK’s international commitments?”
Mr Middleton responded: “It is clear that we do have concerns about agreements that have been made in the past and the need to ensure unfettered access within the internal market of the UK.
“I think questions have been raised about the legality of the processes, whether Executive approval will be required or not in terms of progressing with the individual checks.”
But Mr Kearney said: “The Executive has a legal obligation in relation to these matters as they apply to ourselves. There is a requirement for border control posts to be put in place to create the necessary infrastructure.
“We have heard a lot of media commentary around this. Some of that media commentary has been made by the minister for agriculture himself.
“I think that the committee can be reassured that no documentation – no paper – will be brought before the Executive because all proposals and documentation coming from individual ministers passes through the Executive Office for clearance before being tabled on the agenda.
“The Executive Office will not allow and will resist any kind of proposals being brought forward that potentially put the Executive in a situation where it would be outwith its legal obligations under the protocol.”
Independent unionist Alex Easton asked if the legal advice supplied to Mr Poots would be shared with his ministerial colleagues.
Gary Middleton: “I have not seen any legal advice. I would suspect that the Department of Agriculture when and if they bring forward a paper to the Northern Ireland Executive, that we would see clearly an outline to the reasons why it has been brought forward.
“I would assume that if the minister brings that forward that he would have sought legal guidance as to why they feel that such a decision is necessary from the Executive.”
Mr Easton said: “If there was legal advice that the law was being broken, would you expect every party that was in the Executive to obey the law?”
Mr Middleton replied: “I would expect every party to obey the law. If anything was brought forward to say that we were breaking the law, then of course there is that expectation.”