An operation which sees the M20 motorway in Kent turned into a lorry park had to be implemented because of cross-Channel ferry delays.
The system is used to ease traffic backlog at ports and borders in Kent.
Winds of about Gale Force 8 delayed all sailings from Dover's eastern docks on Wednesday and passengers were told to expect disruption.
Dover Coastguard said tugs were needed to help ferries berth and unberth in rough seas.
Police said Operation Stack was brought in to manage queuing freight traffic, with closures at junctions 11 and 12.
Other traffic was diverted to the A20 where officers said there were three-mile tailbacks on Wednesday afternoon, but that traffic was moving.
A spokeswoman for the Port of Dover advised passengers due to sail to contact their ferry operator for more information.
Earlier, she said the ferry operators affected included
P&O Ferries and SeaFrance to Calais, and NorfolkLine to Dunkerque.
SpeedFerries' fastcraft services from the Hoverport to Boulogne were also disrupted.