Manual passport checks at the main cross-Channel terminals could cause increased traffic delays resulting in congestion, particularly in the Dover area.
It is thought that Operation Stack - where vehicles are held on the M20 motorway - will have to be implemented on a more regular basis.
The new system was introduced on 8 April, 2015, when all outbound travellers leaving Britain will have to have their passports manually checked.
The director general of the Border Force, Sir Charles Montgomery, has admitted that the technology being used to carry out the passport exit checks has yet to be finalised. The British International Freight Association (BIFA) and industry related trade associations are concerned about this uncertainty and the lack of clarity especially with only eight weeks before the system is set to be introduced. It is anticipated the Border Force will take a pragmatic approach and ensure that the new system is only introduced if the technology has been properly implemented and tested.
The checks will involve operators recording passport information on all travellers and passing the details on to the Home Office, which will use the details to identify immigration offenders.