More than half the UK companies importing or exporting goods through the EU border have suffered delays this month, largely because of post-Brexit paperwork, according to a survey.

Nearly a quarter (23 per cent) believe they will run low on stock in the next few weeks unless the border situation improves, according to the survey of supply chain managers by the Chartered Institute of Procurement & Supply.

The delays have been prompted by a combination of bureaucratic requirements now that the UK has left the EU and extra protocols to deal with Covid-19.

Some 60 per cent of the 444 respondents said goods were reaching the UK more slowly from Europe, with 37 per cent reporting delays of several days. The equivalent figures for goods entering the EU from Britain were 45 per cent and 28 per cent respectively.

The managers mostly blamed time lost while customs officials worked through the paperwork. Only around a quarter said they had not noticed any delays at all. The rest of the respondents did not offer an opinion.

John Glen, economist at Cips, said he expected a “worrying” increase in border delays in the short term.

“Traffic through the border since January 1 has been low compared to historical levels, but with December stockpiles depleting it won’t be long before trade traffic increases and more pressure is placed on these new border processes,” he said.

The warning came as Emma Churchill, director-general of the Border Delivery Group in the Cabinet Office, confirmed that outbound traffic through Dover was only running at 71 per cent of the same level last year.

She told the House of Commons public accounts committee that on average 5 per cent of lorries were being turned back before reaching Dover each day because they lacked the right paperwork. That equated to up to 200 trucks over a 48-hour period, she said.

Authorities had issued 636 fines to hauliers for failing to have a Kent Access Permit, Ms Churchill said.

The committee heard examples of delays at the border — including how a lorryload of crisps was held up for two days in Northern Ireland because officials feared it could end up in Ireland.

Meanwhile, Paul Lincoln, director-general of the Border Force, said it issued 40 fixed penalty notices on Monday alone to visitors arriving without a Covid-19 test. Mr Lincoln told the committee that 10,000 checks were carried out, mostly at Heathrow, out of 21,000 people entering the country that day.

Alex Chisholm, permanent secretary at the Cabinet Office, said he was confident that 68 per cent of relevant exporting companies considered they had taken necessary steps to export after Brexit, based on a YouGov survey. But that would imply that tens of thousands of businesses were not ready.

Ministers have stated for months that they want to prioritise the “flow” of goods after Brexit even if that means the loss of some income to the exchequer through tax avoidance.

Jim Harra, head of HM Revenue & Customs, told the committee that £800m of revenue was likely to be lost in 2021/22 because of more lax procedures at the border — although much of this is deferred revenue that would be clawed back later.

Separately, a business survey by the CBI employers group found that Brexit border disruption, Covid-related delays and global shipping sector bottlenecks led to the highest share of UK manufacturers being concerned about a lack of materials and components since 1975.

The index for lack of materials and components as a factor limiting production in the next quarter, rose in January to five times its longtime average.

Experimental data released by Huq, a company which tracks the geolocation of hauliers and passengers through ports, found that in January, port delays rose to the highest level since last March.

That was despite the number of daily ship visits dropping in mid-December and barely picking up in January, according to data published on Thursday by the Office for National Statistics.

In the week to January 17, there were an average of 88 daily visits of cargo and tanker vessels to UK ports, lower than the 103 in the same period in November and down from 125 in the same week a year ago.