The Dover Port Health Authority (DPHA) said the Sevington facility in Ashford, which is 22 miles inland, had not been designed to handle the scale of imports expected, and claimed its position would "create an open door for disease and food fraud”.
The comments come weeks before post-Brexit border rules are brought in on 30 April, which will require many meat, dairy and plant products from the EU to be physically checked at government border control posts (BCPs).
In November, the £147m Sevington facility was chosen by the government as the main BCP for food and plants moved via the port of Dover, which handles a third of all EU trade.
In a letter, Lucy Manzano, the head of the DPHA, which is run by Dover district council, questioned the decision, pointing to "significant capacity and design limitations" at Sevington.
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