Mr Poots responded that he wanted the issue of “unnecessary checks” to be addressed and said trading barriers were not benefiting Northern Ireland.
The Government has threatened to trigger the Article 16 suspension mechanism within the post-Brexit arrangements for Irish Sea trade.
It has set the EU a December deadline to find a solution on the protocol, which was agreed as a way to maintain a free-flowing land border on the island of Ireland after Brexit.
The arrangement effectively keeps Northern Ireland inside the EU’s single market for goods, resulting in some checks for products crossing the Irish Sea from Great Britain.
During ministerial question time at Stormont, TUV leader Jim Allister asked Mr Poots if he agreed that the protocol had caused “substantial diversion” of trade.
He added: “Diversion of trade is one of the grounds on which Article 16 of that same protocol can be triggered.
“If it is triggered will the minister undertake that at that point he will cease all checks at our ports which are being exercised under the protocol?”
Mr Poots said: “I have engaged with my civil servants indicating that they should be looking at the Command Paper that was produced in July as a means of moving forward on this particular issue because trading barriers are not to our benefit and the employment of highly qualified staff in that role takes them away from other important roles.
“So, unnecessary checks should not be carried out at the Northern Ireland juxtaposition with the rest of Great Britain and therefore that action needs to be addressed.”
SDLP MLA Matthew O’Toole asked the minister about the increase in food exports between Northern Ireland and the Republic since the implementation of the protocol.
Mr Poots responded: “I am aware of statistical reports showing large increases in food exports between Northern Ireland the Republic of Ireland compared to 2020. I would add that caution has to be applied to comparisons with 2020 given the impact of the Covid pandemic.
“The increase in trade with the Republic of Ireland is not surprising given the trade barriers that have been put in place between Great Britain and Northern Ireland with the resulting disruption causing businesses difficulties in trading with what is by far our biggest market.
“Hence, I am continuing to seek the removal of all trade barriers within the United Kingdom.”
The minister was also asked about the cost of ongoing legal action over his party’s boycott of North South Ministerial Council (NSMC) meetings, as part of its protest against the protocol.
Last month, High Court judge Justice Scoffield ruled the DUP position unlawful following a challenge by Belfast businessman Sean Napier.
Despite that declaration, the DUP has continued to stay away from previously planned north-south meetings, leading to a further court challenge.
Mr Poots told the Assembly that as the legal action is continuing, he could not update MLAs on its cost.
SDLP MLA Daniel McCrossan said: “Undoubtedly the costs will be significant. Do you accept that your illegal obstruction of meetings of the North-South Ministerial Council undermines the rule of law?”
Mr Poots said: “As it is a matter which is currently before the courts I don’t wish to comment.”
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