All regulatory animal-based food checks have been suspended at Belfast and Larne ports, Northern Ireland's Department of Agriculture, Environment and Rural Affairs (Daera) has said.
It comes after council staff at Larne Port were withdrawn from inspection duties amid concerns for their safety and welfare.
A Daera spokesman said: "On the basis of information received today and pending further discussions with the PSNI (Police Service of Northern Ireland), 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."
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and East Antrim Borough Council staff assisting officials from Daera and UK Border Force with checks at the port were withdrawn from their duties with immediate effect today.
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 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 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 concerns 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 Féin 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 today 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."
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.
"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."