At Dover, where people go through the French border before they board a cross-Channel ferry, French authorities had not yet switched on the machines that will take fingerprints and photos under EES.
However, border officials still had to create profiles for travellers linked to the new system, meaning it was taking longer to get through border checks.
Due to the congestion, traffic leaving the port is being directed onto the A2 only.
Passengers who miss their ferry crossing due to wait times will be able to travel on the next available crossing, the port said.