Brittany Ferries said several of its haulage customers have already switched journeys to the Kent port because of a perception that goods are checked quicker there.
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A ferry firm has accused the Government of putting smaller ports at a disadvantage by focusing investment on Dover ahead of new Brexit customs checks.
Brittany Ferries, which operates from Portsmouth, Plymouth and Poole, said several of its haulage customers have already switched journeys to the Kent port because of a perception that goods are checked quicker there.
New rules from January 1 state that importers must make a full customs declaration on goods entering the UK from the EU or other countries.
Traders will no longer be able to delay completing full import customs declarations for up to 175 days, a measure that was introduced to cope with the disruption of Brexit.
Border control infrastructure at ports was historically funded by the private sector, but the Government has intervened since the Brexit vote in an attempt to minimise disruption.
Brittany Ferries chief executive Christophe Mathieu said the opening of a facility to conduct customs and document checks for hauliers using the Port of Dover demonstrates the “lack of a level playing field”.
He said the building and operation of the Sevington inland border facility near Ashford has been “fully funded by the Government”, whereas taxpayers’ cash has only part-funded a smaller inspection point at Portsmouth Port.
“All of the Government’s focus has been on Dover, ensuring that the facilities there work well, and funding those facilities potentially to the detriment economically and operationally of ports like Portsmouth,” he said.
Brittany Ferries will monitor the time it takes to check lorries using its vessels following the introduction of the new rules from Saturday.
Some of its haulage customers have previously switched to travelling through Dover after experiencing “overzealous checks” elsewhere, according to Mr Mathieu.
Making it even harder to transport goods through other ports may lead to some routes “disappearing” as transport firms operate on small margins, he added.
Tim Morris, chief executive of the UK Major Ports Group, which represents firms operating 40 UK ports excluding Dover, said there is a “very strong political resonance to fears of long lorry queues”, leading to an “over-focus” on Dover.
“For the private sector it’s a distortion of trade, and that makes both operating and attracting new investment more difficult if you’ve got a Government-sponsored player in the market,” he said.
Mr Morris acknowledged that Dover is “very important” but insisted “there are other very important ports too”.
He added: “It is in Britain’s interests that there is a choice of ports, a choice of routes and a choice of freight modes, to give us supply chain resilience for trading to and from Europe.”
Mr Morris said he expects any disruption at ports from Saturday to be minimal as the industry has previously demonstrated it “learns very quickly” when new systems are rolled out.
He added that the “bigger change” happens from July 1, when stricter checks on plants and animals will be required.
A Government spokesperson said: “Through our Ports Infrastructure Fund, we made £200 million available so that more than 40 ports across the UK could put facilities in place to perform customs and biosecurity checks on goods imported from the EU. The approach to checks will be the same at all points of entry wherever goods enter Great Britain.
“The infrastructure needed will vary by port depending on existing facilities and the type of trade they handle. In many cases, this funded infrastructure is now in place at ports and will be ready to be used when border controls are introduced.”