Foyle Port in Derry
The ports are at Foyle in Derry, Belfast, Larne, Warrenpoint and Coleraine.
The letter says it is critical checks are in place, stating such moves are in accordance with the ‘Northern Ireland Protocol’.
Last week Agriculture Minister Edwin Poots said he wanted to pause the work on food and animal controls.
The letter, seen by BBC News NI, is from UK Environment Secretary George Eustice.
It was sent to the most senior civil servant in Stormont’s Agriculture Department.
Mr Eustice writes: “It is my expectation that your department will procure such facilities in accordance with obligations of the Northern Ireland Protocol.”
It adds: “Delivery is critical to mitigate risks to food security, including potentially security of supply, cost to the taxpayer and value for money.
“Compliance is necessary for the continued well-being of people, businesses and communities in Northern Ireland.”
Mr Eustice states that the frequency and level of checks are part of the discussions with the EU.
He states that it is government policy to “minimise checks within the spirit of the Northern Ireland Protocol”.
The letter ends: “My view is that it is now the role of your department to procure the facilities for agri-food checks without delay ”
Mr Poots had previously said he wanted to pause the work at sea ports until he had received clarity, but now the work will go ahead.
Earlier this week he confirmed to the BBC that his department had received a letter from Mr Eustice and the UK department was paying for the work at Northern Ireland’s ports.
He said that work would now commence.
In a statement this week, Northern Ireland’s Agriculture Department said: “There is a binding international agreement passed by Westminster to implement the Northern Ireland protocol.
“DAERA officials are working to implement points of entry in order to meet those requirements as set out by the Defra minister and the UK command paper, The UK’s Approach to the Northern Ireland Protocol.
“Approved points of entry are a legal requirement for the purposes of protecting public health, securing safe food supply and protecting animal and plant health.”
Tenders for the work at a number of sea ports have just been made public and bids are to be made by later this month.
It is estimated that the work could cost about £40 million.
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