The Port of Dover has been a trust port for 400 years, with all revenues going back into it.
The ship arrived in the Port of Dover to undergo the berthing trial earlier.
BBC: Dover trial of animal export ship MV Joline inconclusive
Bob Goldfield, chief executive of the Port of Dover, said the decision was frustrating.
The operator of a ship used to export livestock from the UK has applied to sail from the Port of Dover.
The goods were passed for export at the Port of Dover in Kent because computer systems were down for maintenance on that day.
The Port of Dover said it was experiencing high volumes of traffic and advised passengers without tickets to contact ferry operators before setting out.
Channel crossings to France and crossings between Wales and Ireland have been cancelled and the Port of Dover is closed due to hurricane-force 80mph winds.
It added that a full evaluation of the second trial would be carried out before any final decision was made as to the suitability of the vessel to operate from the Port of Dover.
BBC: Second Dover berthing trial of animal export ship MV Joline
The operator said passengers due to make return journeys on Saturday or Sunday were advised to arrive at the Port of Calais or Port of Dover where their return travel would be honoured by other cross-channel operators.
"We have made it clear that the port of Dover would be the most suitable location, but as the boat being used is unable to dock there currently, Ramsgate is the next best option available, " he explained.
Phase two of Operation Stack is in operation on the M20, meaning coastbound traffic is taken off the motorway at junction eight and lorries heading for the Channel Tunnel or Port of Dover put back, but held in a queue.
It returned to Dover for further tests to assess the port's suitability for live exports as a trial last month proved inconclusive.
BBC: Second Dover berthing trial of animal export ship MV Joline
Part of the M20 in Kent remains closed as police and port officials continue to regulate freight traffic heading for Dover and the Channel Tunnel.
The south coast ports of Southampton, Dover and Portsmouth saw the biggest increase in port activity.
"Developing the port, providing an important contribution to the regeneration of Dover, growing and adding value to the business, were key objectives for the DHB scheme and will continue to be our focus as we remain as a trust port, " he said.
The Conservative MP for Dover, Charlie Elphicke, said as an alternative to the privatisation plans the port could be owned by a community trust, made up of local representatives which would lease the port to an operator.
Dover police estimate that 6, 000 smugglers from all over Britain pass through the port each day.
应用推荐