The alarm was raised over two loyalist groups after food inspections were suspended at Belfast and Larne ports following an “upsurge in sinister and menacing behaviour in recent weeks”.
Graffiti has appeared attacking the impact of the Northern Ireland Protocol – which has created a customs border in the Irish Sea – and describing port staff as “targets”.
Haulage firms have hiked prices by 12 per cent this week and hospitals, schools and prisons have warned of looming problems obtaining food supplies.
Alan McQuillan, a former assistant chief constable in Northern Ireland, said the graffiti had made “direct threats to border staff or staff working at the border posts”.
And he added: “This area is a real hotbed of Loyalist paramilitarism. There are two major Loyalist paramilitary groups there and both of them do represent a real and significant threat.”
Edwin Poots, Northern Ireland’s agriculture minister, from the Democratic Unionist Party, called for calm, and for border staff not to be seen as “enemies” – but warned local people were being hit hard.
“The economic issues are absolutely clear,” he said, adding: “People are having to pay additional costs to bring food in to Northern Ireland.
“And these are going to be passed onto some of the lowest-paid people anywhere in the UK.”
Both Mr McQuillan and Mr Poots blamed the EU’s bungled attempt to control vaccine exports, which – briefly, before a Friday night U-turn – triggered Article 16 to suspend part of the Protocol.
“What has really crystallised this is probably the European Union’s behaviour over the vaccine issue,” Mr McQuillan told BBC Radio 4.
And Mr Poots warned the EU’s “crass act” had made it “difficult for politicians to contain the level of anger that there is”.
He repeated the DUP’s demand for Boris Johnson to invoke Article 16 if necessary and warned things would get worse when ‘grace periods’ for supermarket paperwork and processed foods ended, in April and July.
“The people who are supplying the hospitals, the schools and the prisons have indicated to me, in a meeting, they will have problems supplying those key areas,” he said.
Twelve staff from Mid and East Antrim Borough Council staff, who were helping UK Border Force with checks, were withdrawn from their duties on Monday.
The situation has caused “extreme distress and worry to staff”, the council said, leaving it with “no option but to withdraw them from their duties in order to fulfil its duty of care”,
As well as concerns about the graffiti, it is understood that staff warned people had been spotted taking down their number plate details.
Patrick Mulholland, deputy general secretary of the Nipsa union, which represents Northern Ireland’s port workers, said his members needed to know someone has “got their backs”.
“They first of all tend to be in shock because they suddenly find themselves under a level of threat they would not expect to be under. These are ordinary working people,” he said.