Staff conducting physical checks on animal products entering facilities in Belfast and Larne were withdrawn because of "an upsurge in sinister and menacing behaviour in recent weeks".
NI's Department of Agriculture, Environment and Rural Affairs subsequently confirmed that checks on animal products will be postponed until a full risk assessment is carried out by the police. The EU has since told its port staff not to go to work.
And Alan McQuillan, a former assistant chief constable in NI, warned that loyalist paramilitaries in the areas present a "real and significant threat".
But why are checks carried out in NI, why are loyalists, or unionists, unhappy about the rules and what would they like to see instead?
Graffiti has recently appeared at Larne port opposing the Irish Sea border, referring to employees who work there as "targets" and it being "time for war".
Some workers have also reported suspicious activity including people taking down personal information such as car number plates.
It is not immediately clear who exactly is behind this activity, but last week police in NI said they were monitoring "stress" and "growing discontent" within the unionist/loyalist communities over the Irish Sea border.
What is the Irish Sea border?
As part of the Brexit deal, both sides agreed to a mechanism called the Northern Ireland protocol, which allowed NI to stay in the EU's single market as well as the UK's customs territory.
This meant that goods could continue to flow freely between the Republic of Ireland (ROI) and NI without the need for phyiscal checks – or a "hard" border on the island of Ireland, in a move aimed at stopping a return to the "Troubles".
But because the UK and EU now follow different customs rules, checks are still needed on some products entering NI from the UK.
As a solution, prime minister Boris Johnson's government installed border posts at NI's ports, effectively creating an "Irish Sea border".
Some unionists believe the NI protocol breaches the Good Friday Agreement and poses an existential threat to NI's constitutional status within the UK.
They say the Brexit deal has cut NI adrift from the rest of the UK, pushing Belfast further away from London and closer towards Dublin, paving the way for an "economic united Ireland".
There has been some disruption at NI ports due to increased paperwork and bureaucracy.
As a result of this, a number of supermarkets have reported declining stocks of some products, while other firms have stopped trading with NI altogether.
This had led the Democratic Unionist Party, NI's largest party, to call on the UK government to invoke Article 16 of the Brexit deal, a mechanism that would remove the NI protocol.
The DUP voted for Brexit but opposed the Withdrawal Agreement, which set out the terms of the protocol.
Earlier this month, senior DUP MP Ian Paisley claimed the sea border was an "unmitigated disaster" and urged the UK government to invoke Article 16.
No clear alternative
But it remains unclear what the DUP wants to see replace the Irish Sea border.
Seamus Leheny, a policy manager at Logistics UK, which represents freight operators, said at the beginning of January that those calling for Article 16 to be revoked need to propose a "realistic alternative".
He said: "You can't just walk away from this. I think to invoke Article 16 you'd create more problems compared to what we're facing today."
The government has repeatedly insisted that the problems at ports in NI and elsewhere are temporary.
Mr Johnson has said he will have "no hesitation" in triggering Article 16 of the Northern Ireland protocol if “disproportionate” problems arise as a result of the legislation.
But he did not set out what would replace the agreement in the event that Article 16 is revoked.
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