The construction of the inspection facilities was ordered by Environment, Food and Rural Affairs Minister Thérèse Coffey following the signing of the Windsor Framework.
It is regarded as a clear signal that the British government is pushing ahead with implementation of the revised protocol arrangements agreed in February.
Earlier this week, the EU adopted new rules aimed at simplifying trade between Britain and the north.
The Windsor Framework was designed to assuage unionist concerns about the Irish Sea border. However, more than three months on from the breakthrough, the DUP has yet to endorse the deal.
Work has also begun on what officials have termed "an additional, temporary, product inspection facility" at Belfast Port, which is expected to be operational by October 1.
Whitehall's Department of Environment, Food and Rural Affairs is overseeing the construction of the sanitary and phytosanitary (SPS) facilities at Belfast, Larne, Warrenpoint and Foyle ports. The checks are designed to protect the integrity of the EU single market, which includes the sharing of trade data with Brussels officials.
Stormont's corresponding department – the Department of Agriculture, Environment and Rural Affairs – must comply with the order under legislation passed earlier this year "irrespective of whether any matter has been brought to the attention of, or discussed and agreed by, the executive committee of the Northern Ireland assembly".
Former agriculture minister Edwin Poots attempted to halt work on the port inspection posts in January last year. The High Court later ruled that the move was "politically motivated" and that the DUP minister had breached a legal obligation to implement inspections on goods entering the north.
SDLP Stormont leader Matthew O’Toole said the Windsor Framework was being implemented "whether the DUP boycott the institutions or not".
He said the British government had made "binding legal commitments" to the EU under the revised protocol.
"In order to build trust and ensure progress on the issues dealt with in the Windsor Framework, it was vital that the UK finally show seriousness around meeting those legal obligations," he said.
"Properly constructed and operated SPS facilities will not only meet those obligations, they will help protect Northern Ireland's unique dual market access and the enormous opportunities it presents, not least to local food producers."
Meanwhile, former Brexit Party MEP Ben Habib has conceded that those who campaigned against the protocol "won the debate but lost the battle".
While not advocating the return of Stormont, the property billionaire calls for a reduction in the north's corporation tax rate.
"If the aim is to assure Northern Ireland’s place in the United Kingdom, its leaders must forge a plan for economic and political prosperity," he wrote in the News Letter.