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 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.”