The Port of Dover said it is "deeply frustrated" with "significant delays" surrounding coach traffic due to French issues with checks and the sheer volume.
Additional coach bookings taken by ferry operators during Easter has impacted operations, a statement on the port's website said on Saturday morning.
P&O Ferries also apologised for the wait times for coaches sailing from Dover, while DFDS said it is expecting a busy weekend and advised passengers to allow extra time to complete border and check-in controls.
A statement from the port said: "The Port of Dover is deeply frustrated by last night's and this morning's situation and particularly so on behalf of all the ferry operators' coach passengers who have had to endure such a long wait at the port.
"Whilst freight and car traffic was processed steadily regardless of the additional challenging weather conditions and high seasonal volumes, coach traffic suffered significant delays due to lengthy French border processes and sheer volume.
"Despite considerable pre-planning with our ferry operators, border agency partners and the Kent Resilience Forum, and the success of similar plans for processing substantial numbers of coaches during the most recent half-term period, the additional coach bookings taken by ferry operators for Easter has impacted operations for the port."
The port said food and drink has been provided to coach passengers in the queues, adding: "We offer our sincere apologies for the prolonged delays that people have endured and continue to work with all of our partners to get all passengers on their way as quickly as possible."