UK hauliers have been warned to expect much tougher French customs controls from Monday, raising fears of the first serious border disruption since the new post-Brexit controls were introduced.

The warnings were shared on two conference calls between British industry bodies and UK government agencies on Thursday, according to three separate individuals with knowledge of the discussions.

One said that the French had “read the riot act” to port and ferry operators after initial checks this week showed that almost all the lorries arriving from the UK were not fully compliant with EU trade rules, particularly on phytosanitary (SPS) controls on agrifoods.

The French government said it was not preparing to step up checks from next week, saying it would conduct routine checks as normal.

But UK trade groups and senior Whitehall officials said they were now braced for “more rigorous checks” after a quiet start to the new year. Lorry traffic across the “short strait” between Dover and Calais has been running at just 50 per cent of normal January volumes, said one person with knowledge of the latest figures.

One senior UK official said the government was “holding its breath” for more significant disruption at British ports in the coming days. “We’re going to start seeing a crystallisation in the next couple of days of the pressures building up,” they said.

Rod McKenzie, managing director of policy and public affairs at the Road Haulage Association, said the low volumes were the “lull before the storm”.

“The current low volumes won’t continue,” Mr McKenzie said. “So, unless operators are diligent and border-ready, including getting driver Covid tests, next week could be very challenging for the supply chain.”

Trade groups warn that the combination of the extreme complexity of some paperwork combined with the fact that 85 per cent of drivers crossing the Channel were from the EU side, thereby hampering communications, increased the risk of repeat compliance failures.

Shane Brennan, the chief executive of the Cold Chain Federation, said it was possible for vehicles to obtain electronic authorisations to travel but then still discover that SPS documents they had submitted were not in order on inspection in France.

“The government has this theory that vehicles will only appear unprepared once and the second time won’t do it again. But these processes are so complicated that might be a very optimistic assessment of the situation,” he said.

John Glen, economist at the Chartered Institute of Procurement and Supply (Cips) added that many members had indicated they would return to trading in earnest next week, creating a potential “perfect storm” as full French customs controls kicked in.

A spokesperson for the French ministry that oversees customs said officials at the border had been following the new post-Brexit rules governing trade with the UK since January 1. “At this stage there are few controls happening because the traffic is very low,” he said. “But the new rules have been applied from the first day and have not changed.”

He added: “We do not fix a specific level of controls to be made on shipments coming across the border. The controls depend on the risk posed by the merchandise itself.”

Meanwhile, concerns about problems with goods movements across the Irish Sea continued on Thursday. According to internal UK government figures shared with the FT, 25 per cent of vehicles transiting through the Welsh port of Holyhead to Dublin in the Irish Republic were not border ready.

In another sign of Brexit disruption to established freight routes, ferry operator Stena Line has cancelled 12 sailings on the Holyhead-Dublin and Fishguard-Rosslare routes this weekend and early next week.

Paul Grant, Stena’s Irish Sea trade director, said the drop-off in freight numbers at Holyhead and Fishguard and an Irish coronavirus travel ban on passengers arriving from Britain were behind the cuts. But he added that capacity could be quickly reinstated as and when demand picked up.

Whitehall insiders said the situation in Northern Ireland was the most “worrying”, as haulage groups continued to complain about the shortcomings of the £355m trader support service designed to help hauliers with new paperwork.

Aidan Flynn, general manager of FTA Ireland, representing the country’s logistics industry, warned continued failure to follow the new customs rules could have a “significant impact on trading conditions and the supply chain as a whole” as trade volumes revived.

“No one wants vehicles and drivers to be stuck in port for hours on end,” Mr Flynn said. “It is up to shippers and hauliers to work together to complete all customs, safety and security declarations and pre-boarding notifications in advance of moving to ports.”