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"We get disrupted by the other links in the chain, and their delays flow through to us," Mr Winders said.
International shipping companies were engaged in a massive juggling act, as they tried to maintain their schedules in the face of constant delays and changes, he said.
"This means that some of the vessels that would usually come in to Port Otago weekly may not come one week, and then there will be double the next week.
"They are all moving around the world in rotation and, when things get out of whack, that causes problems for them."
Once a ship arrived in Port Chalmers, it would take only two days for it to be off-loaded and the goods forwarded to the customer, as normal, Mr Winders said.
In order to combat the disruptions, some international shipping lines were bringing in vessels known as "extra loaders", which could transport delayed cargo to its destination.
As Port Otago was predominantly an export port, it needed a good supply of empty containers to keep goods moving through — ships on weekly rotation would drop off "empties" and load up with full containers.
"However, if a ship is delayed a week, then we don’t get the empties, which causes a backlog of goods waiting at the port," Mr Winders said.
"If that happens too often, the port fills up and we get jammed up."
New Zealand was in the midst of peak export season at present, with apples, kiwifruit, meat and dairy "all going strong", he said.
"So, for the shipping companies, it’s a giant juggling act, and the disruptions are a real challenge for the planners."
The team at Port Otago were also constantly adapting to the situation, to keep the supply chain running.
"I can see the disruption going on for some time to come, we could be like this through until Christmas."
On the plus side, New Zealand exports were going extremely well at present, which was very pleasing to see, he said.