Peter Brown was responding to criticism from Taieri Gorge Railway chief executive Murray Bond on the late arrival of Sun Princess on January 2, which resulted in the tourism operator losing 400 customers.
Mr Bond said the business lost tens of thousands of dollars every time there was a cancellation, and questioned why other cities were not left off the vessel's New Zealand itinerary.
"Dunedin has really suffered over the last two seasons with cancellations or late arrivals and has suffered more than any other city in New Zealand," Mr Bond said.
Poor weather across the Tasman resulted in Sun Princess arriving shortly before 4pm - more than eight hours late.
Mr Brown said he understood the financial impact on a business as a result of a cancellation or delay, which had been compounded by Monday being a statutory holiday.
"From a Port of Otago perspective, and a local economy perspective, the cruise ships are really good for us.""The really good thing was that it came into Port Chalmers. They could have omitted Port Chalmers completely."
Mr Brown said the benefits of being the first or last New Zealand port of call for visiting vessels, far outweighed any negative impacts.
"They are coming across the Tasman. They have been at sea for two or three days and the passengers want to get off, so what we see is more passenger get-off at Port Chalmers-Dunedin than they would normally do at any other port."
While the Taieri Gorge Railway "missed out" this time, other businesses had benefited.
Mr Brown said the incidence of late arrivals or cancellations was proportional to the increasing number of ships which visited the city each year.
