A row between Northern Ireland's parties, as well as the Irish government, has erupted after Edwin Poots claimed he could legally stop the checks that have been going on since 2021.
Northern Ireland's agriculture minister has issued an order to halt all post-Brexit checks on food and farming products coming from the rest of the UK.
The agri-food checks at Northern Ireland's ports are required under the terms of the Northern Ireland Protocol, which is designed to avoid the introduction of a hard border between Ireland and Northern Ireland.
Edwin Poots, former leader of the Democratic Unionist Party (DUP), said he will seek an agreement from the power-sharing government on a way forward in the near future.
He said he made the decision based on legal advice but Sinn Fein, the party the DUP shares power with, said it was unlawful and "a stunt".
The Irish government said halting checks would effectively be a breach of international law.
It is unclear whether the senior civil servant in Mr Poots' department, Anthony Harbinson, will comply with the order and it may only become clear once the first ferries arrive at ports on Thursday morning.
Speaking at Northern Ireland's assembly, Mr Poots, whose party opposes the protocol, said: "I have taken legal advice in relation to my position from senior counsel. Earlier today, I received that legal advice.
"The advice concluded that I can direct the checks to cease in the absence of Executive approval."
Westminster refuses to intervene
The UK and the EU have been in talks for months to change the protocol that has effectively created a border in the Irish Sea, angering the pro-British DUP.
Westminster said it will not intervene with the order to halt checks, saying it was a "matter for the Northern Ireland Executive".
Simon Coveney, Ireland's foreign minister, warned: "If a political decision is taken by a minister in Northern Ireland to stop all checks in ports on goods coming across the Irish Sea that is effectively a breach of international law, and I would remind everybody that the implementation of the protocol is part of international law.
"To deliberately frustrate obligations under that treaty I think would be a very serious matter indeed.
"It is essentially playing politics with legal obligations and I certainly hope that it doesn't happen, as has been threatened and described."
Sinn Fein brands order a 'stunt'
Northern Ireland's deputy first minister Michelle O'Neill, of Sinn Fein which supports the protocol, said: "This stunt is an attempt by the DUP to unlawfully interfere with domestic, and international law.
"DUP fixated on their own priorities, which are clearly at odds with where the wider community is at. Health, Jobs, Housing, Cost of living crisis is where the rest of us are focused."
Last week, British Foreign Secretary and Brexit negotiator Liz Truss said the DUP's threats to halt checks were a matter for the Northern Ireland regional government to resolve, rather than for Westminster to intervene.
Ms Truss is due to speak to European Commission vice-president Maros Sefcovic on Thursday, a government spokesman said.