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Checks on goods along the Irish Sea border are expected to stop on Thursday after Democratic Unionist Party minister Edwin Poots called for a halt.
His order is part of the DUP's ongoing opposition to the Northern Ireland Protocol.
Inspections of products from Great Britain into Northern Ireland are part of the post-Brexit agreement.
Sinn Féin, the DUP's power-sharing partners, criticised the move as a "stunt".
Under the deal, checks on goods from Great Britain must take place at Northern Ireland's ports to ensure they comply with EU laws.
Unionist politicians have criticised the arrangements, saying they damage Northern Ireland's place in the UK.
Simon Coveney, the Irish Republic's foreign minister, has warned that an end to those checks would breach international law.
However, the UK government said it would not interfere and that the issue was a "matter for the Northern Ireland Executive".
Mr Poots, who is the Stormont Executive's agriculture minister, said legal advice supported his view that he was entitled to stop the checks.
The dispute centres on whether he needs the wider authority of Stormont to act.
It remains unclear what officials will do on Thursday in light of Mr Poots' order, although pre-Brexit checks on livestock are expected to continue.
Northern Ireland Deputy First Minister Michelle O'Neill, of Sinn Féin, said the move was an attempt by the DUP to "unlawfully interfere with domestic and international law".
Under power-sharing arrangements, if a matter was put to the executive, it would need an agreed approach from both the first and deputy first minister for changes to be made.
But Mr Poots believes the checks are unlawful and cannot continue without approval from the Stormont Executive.
Last week, his attempt to force an executive rethink on the issue was blocked by Sinn Féin.
Mr Poots had sought executive support for the checks continuing, ahead of a legal challenge by loyalist blogger Jamie Bryson.
The DUP minister argued the challenge made clear that checks must be approved by all ministers as they are controversial and cut across various departments.
A spokesperson for Belfast City Council, which is responsible for ensuring Belfast Port meets environmental health standards, said it would engage with elected representatives and statutory partners on Thursday "and assess the situation at that point".
The BBC has also contacted the UK's Department for Environment, Food & Rural Affairs for a response.
The Manufacturing NI trade body said it was advising members to continue to enact the measures.
Regardless of events, the legal and administrative advice is that these are international obligations on traders and they should continue to meet those obligations whether or not there’s a guy with a hi-vis to greet them at the Port.
— Manufacturing NI (@ManufacturingNI) February 2, 2022The BBC is not responsible for the content of external sites.View original tweet on Twitter
BBC News NI's economics & business editor John Campbell said it is as yet unclear what businesses will do.
Business leaders have previously told politicians that trading issues needed to be resolved as "a matter of priority".
Political reaction
Foreign Secretary Liz Truss is expected to speak to EU Commission Vice-President Maroš Šefčovič when they meet on Thursday.
Northern Ireland Secretary Brandon Lewis said there was no orchestration between the government and the DUP over Mr Poots' decision.
Speaking to ITV's Robert Peston, he said he first found out about the move when Mr Poots announced it, adding that the decision was a "matter for the Northern Ireland Executive" and "within their legal remit".
Irish Foreign Minister Simon Coveney described moves to "deliberately frustrate obligations" under the post-Brexit agreement as a "very serious matter ".
An EU diplomat told BBC News the move "won't do the UK's reputation any good" and questioned the decision's legality.
Sinn Féin's Michelle O'Neill tweeted that the DUP was "fixated on their own priorities, which are clearly at odds with where the wider community is at".
Her party maintains that Stormont has a legal obligation to enforce the checks, and that the executive agreed in May 2020 to designate Mr Poots' department to perform those controls.
The Alliance Party's John Blair said it was "not a time for causing further disruption", adding that his party would consider "very carefully" before deciding on any legal challenge.
Matthew O'Toole, the SDLP's Brexit spokesperson, said the order was "outrageous" and that the public was more concerned with other matters, adding it would "not command the support of the Assembly or the Executive" and would be challenged.
However, the move was welcomed by Traditional Unionist Voice (TUV) leader Jim Allister, who said the protocol's implementation was "never compatible" with Northern Ireland's position within the UK.