Shipowners say queues could be five miles long at peak times when the measures enter force in three weeks, the Guardian reported.
Checks are being imposed on tourists and lorry drivers as part of a pledge made in 2010.
Ferry operators says immigration authorities have refused to allow them to tackle the queues by relaxing the rules on busy days.
The UK Chamber of Shipping said a trial conducted in November showed that the exit checks will almost double the average check-in time for passengers.
