People arriving for cross-Channel sailings on Wednesday were forced to wait as long as three hours to pass through French checks.
By 1.45pm the waiting time had been cut to two hours, the port said.
Passengers arriving at the port are processed by Police aux Frontieres (PAF) – French border workers – before boarding ferries.
Those who miss booked departures because of the queues were put on the next sailing with space available.
A spokeswoman for the port said: “The additional processing time today is a result of staff sickness within Police aux Frontieres.
“All teams are working hard to get everyone on their way as quickly as possible.
“We advise passengers to check with their chosen ferry operator for travel updates.”
Enhanced passport checks following the UK’s withdrawal from the EU have significantly increased processing times at Dover.
Port bosses have taken a series of measures aimed at minimising queues.
