There have been calls for an urgent Executive meeting on Friday night after DUP Agriculture Minister Gordon Lyons ordered his officials to halt construction of permanent inspection facilities for post-Brexit checks.
Mr Lyons ordered a stop to the construction of inspection posts for checks on agri-food goods arriving in Northern Ireland from Great Britain.
Ongoing Irish Sea trade checks, which are taking place at existing repurposed port buildings and other temporary facilities, will continue.
Mr Lyons's decision relates to ongoing work on new purpose-built inspection facilities at ports like Belfast and Larne.
He has also stopped further recruitment of inspection staff for the port facilities and ordered an end to charges levied at the ports on traders bringing goods from GB into Northern Ireland.
Three Executive ministers have formally requested an emergency Stormont executive meeting on Friday night in response to Mr Lyons's move.
Sinn Fein Finance Minster Conor Murphy, SDLP Infrastructure Minister Nichola Mallon and Justice Minister Naomi Long have penned the joint letter to executive colleagues requesting the urgent meeting.
The letter, seen by the PA news agency, states: "This controversial and cross cutting matter requires the Executive to meet as a matter of urgency."
Deputy First Minister Michelle O'Neill noted Mr Lyons's predecessor and DUP colleague Edwin Poots had also attempted to halt construction last year but stepped back from that position due to the legal obligations attached to the Withdrawal Agreement.
She said on this occasion "his Permanent Secretary took forward the Executive's responsibilities".
"The protocol is a consequence of Brexit. The DUP championed Brexit and must own the consequences. Business and society need certainty, not stunts," Ms O'Neill said.
Mrs Mallon accused the DUP minister of "using political office for divisive stunts" and said the decision could not be taken without Executive agreement.
A UK Government spokesman said it was "a matter for the Northern Ireland Executive" and "we remain in close contact with them".
Mr Lyons told the PA news agency: "I've just let executive colleagues know that today I instructed my department to halt work on a range of issues relating to work at the ports.
"This is in and around a number of areas, first of all further infrastructure, any further infrastructure builds; the additional recruitment of staff; and also the charging at the ports."
The decisions come amid the ongoing controversy over disruption caused by the Northern Ireland Protocol, which governs Irish Sea trade post-Brexit.
Unionists are angry at the protocol's requirement for checks on many goods entering Northern Ireland from the rest of the UK.
They claim it has driven an economic wedge between the region and Great Britain, and has undermined the Union as a result.
Mr Lyons said his move was in response to the "practical difficulties" caused by the Protocol.
He cited uncertainty over the movement of goods when grace periods currently limiting protocol bureaucracy end at the start of April.
He said: "We don't know what the movement of retail goods from Great Britain into Northern Ireland is going to look like, we don't have the support in place through the digital assistance scheme yet either, and all of the SPS (sanitary and phytosanitary) issues around the end of the grace period are just so uncertain and it's real nightmare for us and it's going to be causing us an awful lot of problems."
Mr Lyons said his officials have been warning him that the port control posts are unlikely to cope when the grace period exempting retail agri-food goods from EU export health certification ends on March 31.
He said supply chains into Northern Ireland were also unlikely to be able to hold up when the regulatory red tape increases in April.
"The risk to Northern food supply in those circumstances will remain high so there's a lot of practical difficulties with all of this and that's causing us a huge amount of uncertainty," he said.
The minister told PA there was need for the UK and EU to find "permanent solutions" to the issues caused by the protocol.
"It's a real concern to us heading towards the end of the grace period, so we need that certainty from the EU and the UK," he said.
The Agriculture Minister said the UK's Internal Market Act had compelled him to act with special regard to Northern Ireland's place within the UK's internal market.
Asked about his obligation to fulfil the UK's responsibilities under the Withdrawal Agreement, Mr Lyons insisted he was acting in a "reasonable and proportionate" manner in response to the uncertainty around the protocol.
He highlighted that the UK Government had acknowledged there were problems with the trading arrangements.
"I think this is a reasonable and proportionate step to take," he said.
Mr Lyons said the NI Protocol needed to go.
"My own point of view is I think the Protocol needs to be scrapped, it is not working," he said.
"The evidence we have so far shows it's not working and it's only going to get worse at the end of the grace period."