It comes after counter-terrorism police put out a national request for enhanced security checks at UK ports.
Controversial Brexit motorway measure Operation Stack has been activated so lorries can line up to enter the port.
The “emergency measure” is designed to prevent gridlock on Kent’s road network.
Pictures show long lines of HGVs stacked up into the busy port on Wednesday.
It comes after a police operation saw all vehicles and passengers since Tuesday checked as part of a wider operation in Kent and on all short strait routes.
The policing operation has now been stood down and border control checks are returning to normal, Kent Police said.
A spokesperson for Counter Terrorism Policing said: “We can confirm that a request was made on 15 September by Counter Terrorism Policing nationally for enhanced security checks to be carried out at UK ports.
“This was in relation to ongoing operational activity and this requirement has since been stood down.
“We would like to reassure the public that there is no threat to public safety in relation to this activity and thank all those affected for their co-operation and understanding.”
But the delays to transit meant huge queues started to build up into the port and the decision was made to activate Operation Stack.
The traffic measure is now in place on the coast-bound carriageway of the M20 between junctions eight and nine.
A spokesperson for the Port of Dover said: “We are working with our ferry partners to keep the traffic moving and we would like to apologise for any inconvenience caused to our customers and local community.”
