A claim that the UDA was behind threats that led to Irish Sea border checks being suspended in Larne was introduced by the council chief executive, it is understood.
Anne Donaghy is said to have made the claim at a closed Mid and East Antrim council meeting earlier this week.
The meeting came after the appearance of threatening graffiti and claims that car registrations had been taken down.
Earlier this week the PSNI said there was no suggestion of involvement by loyalist paramilitaries and no evidence to support claims that licence plate numbers had been recorded.
It emerged that police have now provided a "threat assessment" to the council.
Officials last night failed to provide details of the assessment.
“Council has a very low threshold concerning threats and the safety of its staff, and will always take decisive action to prioritise the safety and wellbeing of employees," a spokesman said.
“We have just received the threat assessment from the PSNI and we are currently coordinating our risk assessment along with key stakeholders, including DAERA, PSNI and our staff.”
When asked about the threat assessment provided to the council, the PSNI said: "We have nothing further to add to what ACC McEwan said on Tuesday".
Elected representatives at the DUP-dominated council later voted to withdraw 12 staff members involved in carrying out physical checks at Larne Port.
DUP agriculture minister Edwin Poots later ordered that Department of Agriculture, Environment and Rural Affairs (DAERA) staff be withdrawn from both Larne and Belfast ports.
It emerged during a meeting of the Stormont agriculture committee yesterday that on Monday evening Mr Poots rang permanent secretary Denis McMahon to ask for departmental staff to be stood down.
Assembly members were told that during the call Mr Poots said that the PSNI had not grasped the extent of the threat to staff.
"He stated that he was very concerned about the risk posed to staff," Mr McMahon said.
"He was not convinced that the PSNI had a full understanding of the risk based on the continuous feedback he had been receiving and he emphasised the duty of care of officials to staff, and noted that Antrim council was already taking action and was clear that as DAERA minister action needed to be taken to protect staff.
"That's something I take very seriously and that's a unique situation, I have to say, when you're getting that kind of feedback."
North Antrim Sinn Féin MLA Philip McGuigan said he was "deeply concerned after the evidence from the permanent secretary of the department, that despite genuine fears caused by disgraceful graffiti, the decision to remove staff from Larne ports may have been politically motivated.
"The police have clearly put their assessment of any threat level into the public domain and it consists of graffiti and social media activity," he said.
"They have stated they have no evidence beyond that, and refuted claims made at a Mid and East Antrim council meeting."
Meanwhile, a spokesman for DAERA confirmed last night that checks were suspended at Warrenpoint Port on Tuesday "following discussions with partner organisations and staff".
However, a spokesman at nationalist controlled Newry and Mourne council said its employees are continuing to carry out checks at the port.
"This function has not been suspended and none of the council’s staff have been withdrawn from the port,” a spokesman said.
A spokesman for Belfast City Council confirmed its staff had not been withdrawn yesterday and that they were carrying out "documentary checks" at Belfast Harbour.
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