An "upsurge in sinister and menacing behaviour in recent weeks" has led to all physical Brexit checks to be suspended at Belfast and Larne ports.
It comes after council staff at Larne Port were withdrawn from conducting full regulatory animal-based food checks amid concerns for their safety and welfare.
A spokesman for Northern Ireland's Department of Agriculture, Environment and Rural Affairs (Daera) said the decision was made following discussions with the PSNI (Police Service of Northern Ireland).
"The situation will be kept under review and in the meantime full documentary checks will continue to be carried out as usual," they said.
Twelve Mid and East Antrim Borough Council staff assisting officials from Daera and UK Border Force with checks at the port were withdrawn from their duties with immediate effect on Monday.
The decision came as graffiti appeared in the area last month referencing tensions about the Northern Ireland Protocol, the post-Brexit arrangement for the Irish border, and describing port staff as "targets".
There have also been a number of daubings in Belfast amid anger at the Protocol, with a raft of new checks on goods arriving at ports from Great Britain introduced at the start of the year.
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The council said the situation has caused "extreme distress and worry to staff", and it had "no option but to withdraw them from their duties in order to fulfil its duty of care".
It apologised for any disruption but said "the safety and wellbeing of staff is of paramount importance".
In addition to concerns over graffiti it is understood staff expressed concerns that individuals had been spotted taking down number plate details.
Sinn Fein councillor James McKeown said: "Our staff will step away from this work and will only return when we are totally satisfied it is safe and right for them to do so.
"There are simmering tensions within the local community at present and we will not stand by and let our staff be targeted when they are just doing their jobs."
PSNI Assistant Chief Constable Mark McEwan said force officials will meet partner agencies later to discuss the situation.
He said: "The safety of staff working at points of entry is of the utmost importance to us. Where we have any credible information we will share that with our partners and take the appropriate action.
"We have increased patrols at Larne port and other points of entry in order to reassure staff and the local community."
Police last month warned that discontent in loyalist communities was "growing" over the Northern Ireland Protocol, which was designed to avoid a hard border on the island of Ireland after the UK's exit from the EU.
It is designed to allow Northern Ireland to follow the EU's customs rules and has caused delays at ports because of new declarations and checks on goods coming from Great Britain.
The DUP has been vociferous in opposition to the Protocol's operation.
The party's North Antrim MP Ian Paisley condemned the threats to staff but said the Protocol was "bound to cause these problems".
"Such tactics have no place in a democracy," he said.
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Analysis: A disturbing throwback to the Troubles - now is the time for cool heads to prevail
By Stephen Murphy, Ireland correspondent
Just a few days after the EU's Article 16 fiasco, the Northern Ireland Protocol (a very key part of the Brexit deal) is at the centre of another storm, this time an altogether more sinister one.
The sudden withdrawal of staff carrying out physical Brexit-related checks on animal products at two of Northern Ireland's ports, amid threatening graffiti and reports of registration plate details being taken, is a disturbing throwback.
Intimidation of workers was extremely commonplace - on all sides - during the darkest days of the Troubles.
This new threat has been condemned by leaders from across the political divide, including the DUP, which still maintains the Protocol must be scrapped, but through political means.
The Protocol, its supporters say, offers Northern Ireland a uniquely beneficial economic position; one foot in the UK, one in the EU single market.
But it also requires a raft of new checks on trade between Northern Ireland and Great Britain, and therein lies the problem.
There's no doubt that some loyalists feel angry and betrayed since the Brexit deal was finally completed, and regard the metaphorical "border in the Irish Sea" as a schism in the sacred Union.
It appears a small few - and the PSNI has yet to release much detail about the perceived threats - have now resorted to intimidatory tactics to express that frustration.
Until the police can fully evaluate the credibility of any threats, it's important not to give too much oxygen to the actions of what is undoubtedly an unwelcome minority.
But authorities have taken the situation seriously enough to suspend the checks, which will have knock-on effects.
The swift condemnation from unionist leaders is to be welcomed - now is a time for cool heads to prevail to resolve the latest unforeseen consequence of the tangled Brexit process.