Checks on animal and food products at Larne and Belfast ports have been suspended amid concerns for staff safety.
The Department of Agriculture said this was pending talks with the PSNI.
This comes after Mid and East Antrim Council withdrew staff from Brexit inspection duties at Larne Port over security concerns.
Graffiti opposing the Irish Sea border has been painted in some loyalist areas of Northern Ireland in recent days.
The mayor of Larne, the DUP’s Peter Johnston, said the council decision had been taken due to “menacing behaviour” referencing growing tensions over the NI Protocol.
The BBC understands the PSNI is due to meet Mid and East Antrim council and officials from Stormont’s Department of Agriculture, Environment and Rural Affairs (Daera) on Tuesday morning to discuss the threats to workers at Larne and Belfast ports.
The Northern Ireland Executive will also discuss the latest developments.
Police said they have increased patrols at Larne port and other “points of entry”.
“The safety of staff working at points of entry is of the utmost importance to us,” the PSNI tweeted.
“Where we have credible information we will share that with our partners and take appropriate action.”
The BBC has asked the EU for comment on the withdrawal of staff and security fears.
In its statement the Department of Agriculture, Environment and Rural Affairs said: “On the basis of information received today and, pending further discussions with the PSNI, Daera has decided in the interests of the wellbeing of staff to temporarily suspend physical inspections of products of animal origin at Larne and Belfast.
“The situation will be kept under review and in the meantime full documentary checks will continue to be carried out as usual.”
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