The Port of Dover has declared a "critical incident" due to high volume of traffic and delays.
P&O Ferries and DFDS Seaways also reported delays to ferry and coach services, citing bad weather and hold-ups at French border controls as partly responsible for the queues.
The lengthy queues come as thousands of passengers prepare to travel through the port during the holiday period.
Coaches full of children on a school trip were said to be stuck in delays for nearly 11 hours this morning.
One parent tweeted to P&O: "My son and his school have had almost 11 hours wait and still not at passport control yet. Then a 14 hour drive to Austria when they do get to France.
"More information is needed about how you propose to get things moving now. Your updates are good for nothing."
Another passenger posted: "We've been here 5 1/2 hours and no prospect of moving. So frustrating and clearly a foreseeable situation. You knew how many you were expecting!"
And a third said: "Why are you delaying coaches full of children for hours and hours???"
Are you caught up in the delays? Please email us at webnews@mirror.co.uk
This morning, the port said it was "deeply frustrated" that coach traffic was suffering "significant delays".
It said in a statement: "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.
"Through the ferry operators and the port, food and drink has been provided to those coach passengers caught up in the border queues.
"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."
P&O Ferries also apologised on Twitter, saying an extra sailing has been scheduled this evening in an effort to clear the backlog.
It added that "the time it is taking to process each vehicle at French border controls" was causing the delay.
DFDS Seaways was reporting delays of up to two hours this evening due to "winds in the Channel".
On Twitter they said: "We know it's really busy today and we want you to know that we are doing all we can to get all customers on their way as quickly as possible.
"We know this isn't the ideal start to your trip but our teams are ready to welcome you onboard once checked in."
Last year CEO of the Port of Dover has warned the port could face "significant and continued disruption for a very long time" post-Brexit.
Doug Bannister has told MPs he has been invited to Calais, France to view tests for the European Union's incoming Entry/Exit System (EES).
He said the port has not been given any details of the scheme's rules but expressed concern it could cause "significant and continued disruption for a very long time" following its planned introduction in May 2023.
It is expected to involve travellers from non-EU countries such the UK having their fingerprints scanned and a photograph taken to register them onto a database the first time they enter a member state.
The system is a key part of the UK's post-Brexit relationship with the EU, and will determine how smoothly travel to the bloc will be in the future.
Over the past year there have been huge queues snaking miles out of Dover, despite many Tory MPs such as Jacob Rees-Mogg insisting there would be no issues at the port if the UK voted to leave.
“We will maintain a free-flowing border at Dover," he said during the campaign. "The delays will not be at Dover, they will be at Calais."
