A new system for customs checks at ports is “completely on track” and will be operating fully by the time of Brexit, according to a senior civil servant.

MPs have previously expressed concerns about whether the new system would be up and running before the UK’s departure date in 2019.

Jon Thompson, Chief Executive and Permanent Secretary, HM Revenue and Customs, told MPs on the Defra select committee this week: “The CDS (Customs Delivery System) is completely on track and we have absolute confidence that it will be ready by January 2019.

"The project has met all of its deadlines this year. There has been some misunderstanding - this is not a system that you flick a switch with in 2019, there has already been some migration.

"I have absolute confidence but as I have said, I will never give an absolute guarantee on a technological project.”

Currently, there were 55m customs checks at points of entry into the UK and that could rise to 250m and the system was built to cope with 300m, said Mr Thompson.

Meanwhile, there was a warning from business chiefs that uncertainty surrounding the terms of the UK’s departure from the EU was costing trade in the UK.

Duncan Brock, who represents the logistics industry, told the committee: “The biggest implication is the uncertainty. They need to plan for the future and the biggest problem is the uncertainty and whether they should stay with UK suppliers or replace them.”

A real concern was the possibility of long delays at ports, he said.

Meanwhile, Tim Waggott, the chairman of the Port of Dover has called for the UK to join the Common Transit Convention.

This is an arrangement for moving goods between EU member states and other countries, including Iceland, Norway, Switzerland, Macedonia and Serbia.

It is supposed to make it easier to move products from one country to another via a third country that is not necessarily an EU member.

Mr Waggott said: “The UK must apply to become a member of the Common Transit Convention so that freight vehicles continue to move between EU and non-EU countries - of which the UK will be one - with minimal friction and with the focus being on origin and destination.”