The congestion happened after Police Aux Frontières, the French equivalent of Border Force, began trialling new immigration checks.
Lorries were backed-up in long queues up to junction 11 on the M20 as they attempted to enter the Eurotunnel entrance near Folkstone.
It comes after the Government warned of queues of up to 7,000 lorries last month.
A spokesman for Getlink, which operates the Channel Tunnel, said: “The backlog (of traffic) built up this morning during tests conducted by the authorities in preparation for Brexit.”
The spokesman said on Tuesday afternoon that traffic was again flowing “smoothly” through the terminal and services were operating as normal.
It is understood that further intermittent border tests will be carried out before the Brexit transition period comes to an end on December 31.
Photographs showed dozens of freight lorries queued along the M20.
A statement from Highways England said that the delay was caused by a trial of new software.
“The Port of Dover has informed us that new trial software for border checks has been identified as causing the delays, meaning 100% checks are under way", they said.
It said the test took place between 6am and 3pm on Tuesday and was carried out by Police Aux Frontieres, with tests also conducted at the Port of Dover.
Highways England tweeted: “M20 coastbound at J11 Westenhanger – the entry slip is now closed due to heavy congestion in the area due to delays at Eurotunnel.
“Due to the heavy congestion with HGV’s at this location, for safety reasons we have also closed the exit slip at J11 Westenhanger due to the amount of lorry’s parking up along the hard shoulder all the way back to exit slip.”