Local authority staff who suspended their inspection work at Larne Port in Co Antrim earlier this week after claims of intimidation are returning to work this evening.
The decision follows a PSNI risk assessment given to Mid and East Antrim Borough Council.
On foot of the local authority move earlier this week, Agriculture Minister Edwin Poots replicated the action that affected both Larne and Belfast ports.
The Borough Council statement said: "Mid and East Antrim Borough Council staff will return to their inspection duties at Larne Port this evening following the completion of a PSNI threat assessment and subsequent risk assessment by the Council.
"The health and safety of our staff remains our top priority."
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The Department of Agriculture, Environment and Rural Affairs has not yet made a decision on the return of its staff.
A spokesperson said: "The department has received the findings of the formal threat assessment from the PSNI and is currently considering it alongside its own internal risk assessment.
"Any decision to recommence full checks will be informed by both documents."
European Union officials overseeing the implementation of the new checks were also withdrawn from duties on Monday.
Inspections on animal-based produce arriving from Britain, which are required under the contentious Northern Ireland protocol, were suspended at Belfast and Larne ports after menacing graffiti appeared.
Police blamed the graffiti and online comments on disgruntled individuals and small groups and have made clear there is no evidence of wider paramilitary involvement in threats.
The council workers' return to duties was announced as the European Commission said it was exploring all "flexibilities" available within Northern Ireland's post-Brexit trade deal.
President Ursula von der Leyen said she recognised particular concern around the health certification of imported food products.
The DUP has vowed to scrap the Northern Ireland Protocol following disruption to some supplies from the rest of the UK earlier this year.
Ms von der Leyen told Northern Ireland Assembly Speaker Alex Maskey: "I can assure you that the Commission has been exploring all flexibilities available under the applicable rules of Union law and within the framework of the protocol, in order to facilitate the implementation of the protocol, whilst fully protecting the integrity of the Union's single market and customs union."
First Minister and DUP leader Arlene Foster has said unionist frustrations at the trade border in the Irish Sea must be channelled through constitutional means.
PSNI Chief Constable Simon Byrne warned of a "febrile" atmosphere.
Mrs Foster's sentiment was echoed by Taoiseach Micheál Martin who said parties needed to "dial down the rhetoric" over the protocol amid rising tensions.
Ms von der Leyen said: "In some areas of particular concern (e.g. as regards the health certification required for the import of food products into Northern Ireland, import of meat products subject to a ban on imports from third countries and export procedures for goods moving from Northern Ireland into Great Britain), the Union has accepted specific practices, set out by the UK in unilateral declarations issued at the Joint Committee meeting of December 17 2020.
"These unilateral declarations provide for the undisrupted supply of goods and a smooth start to the application of the protocol, subject to conditions, also set out in these declarations of the UK, which are meant to ensure that such flexibilities in the immediate time after the end of the transition period do not create risks for the integrity of the single market."
Supermarket shelves were partially emptied of fresh goods at the start of the year and some businesses based in Britain were ill-prepared for the extra paperwork required when shipping goods to Northern Ireland.
Some parcel deliveries have also been affected and a grace period light-touch regulation of supermarket goods and surrounding the use of customs declarations is due to end later this year.
Mrs Foster said more than 100,000 people had signed her petition to parliament in London calling for unfettered trade from the rest of the UK.
She added: "We have made the case to the prime minister and now the people have made a very public appeal to the government of their country to act.
"This is not the time for more words and drawn-out processes.
"This is time for affirmative action to ensure that there is an unfettered flow of goods within the UK single market."
Sinn Féin's Caoimhe Archibald welcomed the commission president's commitment.
She said: "This shows that the EU is willing to work on practical solutions to the remaining problems which have resulted from Brexit and our exit from the EU.
"While we condemn the events of last week relating to Article 16, we are assured that the EU have learned lessons and are committed to making the protocol work.
"We call on the British government to show the same resolve by committing to proper solutions to the practical issues."
Additional reporting PA