HMRC’s new computer system to monitor customs declarations may be unable to cope with Brexit, according to a Whitehall official.

Prime Minister Theresa May declared last week that Britain would leave the customs union when the country leaves the European Union in 2019, meaning goods leaving and arriving could be subject to customs declarations.

The Times reported that this could see an increase of around 90 million to 390 million declarations a year by 2019 as EU goods movements are classed in the same as way as imports and exports from third countries.

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The current Customs Handling of Import and Export Freight (Chief) system was designed to handle 50 million filings a year, while the new Customs Declaration Service (CDS) had been intended to cope with just 100 million.

The project, which is due to enter service in 2019, was flagged as “amber” under an official traffic-light warning system used for major projects.

A Whitehall source told The Times: “It’s fair to say that Chief and what to do about its replacement is one of the more horrendous problems right now”. 

HMRC, which has already spent £40 million on the project, said that it could cope with the new demand, despite the uncertainty that still surrounds Brexit.

A spokesman said: “The new system will support any changes to legislation, redesigned business processes and increased volumes of transactions.”

“HMRC is prioritising the delivery of CDS to make it ready by January 2019. For a period of time, during the cutover and migration phase, we are planning for the two systems (Chief and CDS) to operate in tandem at the border.

“This would provide extra contingency should we need it to ensure that the UK has a robust border declarations service.”

Despite there being no legal requirement to make customs declarations, business figures argue that it would be the only way to manage a new tariff regime.

A report from the joint consultative committee, the government-industry body that oversees border issues, warned: “The possible reintroduction of customs declaration requirements and frontier controls could potentially cause major disruption at the border, particularly at . . . ferry ports and for trade using the Channel tunnel.”