Hauliers waiting for their paperwork to clear during Brexit custom checks face a £50 ($68) an hour fine.
Truckers have been told that from 1 February, after the first two hours of waiting at the nine sites for the green light, they will be charged £50.
The move is to minimise disruption at the ports, as hauliers wait for their paperwork to clear at special “inland border facilities.”
Since 1 January, the new Brexit system and sheer volumes of the paperwork is said to have caused confusion and delays at borders.
Meanwhile, truckers have said they are experiencing waits often far longer than two hours, and have said they already face extra charges.
In December, Kent County Council was given new powers to clamp and fine lorries in certain areas. Those entering the county need Kent Access Permits and face £300 fines for not having them.
But HMRC defended the planned charges, saying they would not be levied if checks take over two hours, but hauliers have raised questions on how this would be enforced.
“If hauliers remain onsite without a legitimate need then charges will be applicable in line with arrangements currently operated at ports,” a HMRC spokesman said.
HMRC added that social distancing was “in place at all sites” and concerns about welfare provisions for drivers would be investigated.
The government has promised to “redouble” efforts to inform traders of the paperwork required now that the UK is outside of EU rules.
Last week, senior minister Michael Gove warned UK businesses to brace for “significant disruption” at ports. Gove said on Friday that disruption at Britain's border had not been "too profound" yet.
He especially warned on the impact at the French border. "It is the case that in the weeks ahead, we expect that there will be significant additional disruption — particularly on the Dover-Calais route," the cabinet minister said.
On Saturday, in a letter to Ireland’s premier Micheal Martin, the Freight Transport Association of Ireland (FTAI) warned of the consequences of the impact of Britain leaving the EU unless the government takes action to assist the industry trying to bring goods into the country.
It comes as Ireland last week said it was temporarily easing Brexit customs checks on imports from Great Britain after hauliers and firms warned of goods shortages and gaps on supermarket shelves.
The Brexit red tape had also caused issues for shipments into Northern Ireland, despite government assurances that there would be no border down the Irish Sea.
Britain which officially left Europe in January 2020 had been trading on EU terms up until 31 December last year.
The UK clinched a last-minute Brexit agreement with the bloc on Christmas Eve, which will see tariff-free and quota-free trading between the pair.
Under the agreement, food and goods imported into the UK from third countries and then shipped to the EU will face charges. The deal also introduces new customs checks and paperwork at the border.
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