Northern Ireland's Department of Agriculture, Environment and Rural Affairs (Daera) said on Monday it had decided "in the interests of the wellbeing of staff to temporarily suspend physical inspections of products of animal origin at Larne and Belfast" pending further discussions with the PSNI.
A Daera spokesman said: "The situation will be kept under review and in the meantime full documentary checks will continue to be carried out as usual."
Agriculture Minister Edwin Poots said he had taken the decision to withdraw personnel at the ports in consultation with his staff.
PSNI Assistant Chief Constable Mark McEwan said force officials would meet partner agencies to discuss the situation.
"The safety of staff working at points of entry is of the utmost importance to us," he said. "Where we have any credible information we will share that with our partners and take appropriate action.
"We have increased patrols at Larne Port and other points of entry in order to reassure staff and the local community."
It comes after council staff at Larne Port were withdrawn from inspection duties.
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and East Antrim Borough Council staff assisting officials from Daera and UK Border Force with checks at the port were withdrawn from their duties with immediate effect on Monday.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 council said the decision was made following an "upsurge in sinister and menacing behaviour in recent weeks".
Graffiti appeared in the area last month referencing tensions about the Northern Ireland Protocol 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.
The council said the situation had 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 and carry out a full risk assessment with the PSNI, Food Standards Agency and Daera".
It apologised for any disruption but said "the safety and wellbeing of staff is of paramount importance".
In addition to fears over graffiti, it is understood staff expressed concerns that individuals had been spotted taking down number plate details.
Mayor of Mid and East Antrim, Peter Johnston, said: "We have seen what I would describe as deeply troubling graffiti and a very notable upping of community tensions towards the NI Protocol, particularly in recent days.
"The health and wellbeing of our staff is always this council's number one priority and that is why the decision has been taken to withdraw them from their work at the port with immediate effect until we have very real assurances and full confidence that they can go about their duties without fear, threat or concern for their wellbeing."
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."
Police last month warned that discontent in loyalist communities was "growing" over the Northern Ireland Protocol, which is designed to allow the country to follow the EU's customs rules and has caused delays at ports because of new declarations and checks.
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.
"This is the sad reality of those who imposed terms on Northern Ireland without the consent of the delicate community balance which exists here. The protocol was bound to end in tears and here we have society's structure falling apart.
"When (former Irish premier) Leo Varadkar shamefully distributed copies of border posts being blown up in Newry 30 years ago around EU Commission members, he demonstrated that violence and the threat of violence has a seat at the table.
"At the heart of progress in Northern Ireland has been cross-community consent.
"Those who thought they could impose something against the will of every unionist are now reaping the seeds of division they have sown.
"The protocol was bound to cause these problems given the triumphant approach by republicans and nationalists and the wilful ignorance that 50% of the population was opposed to the protocol.
"It's time for the Government to step up and invoke Article 16, set it aside and let's get back to proper trade without restrictions."
Join our commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies