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Strong winds at Taiaroa Head prevented Pacific Dawn and its 2050 passengers and 900 crew from arriving at Port Chalmers from Milford Sound yesterday morning.
The city could expect one or two cancellations in a season, "but to get three is highly unusual", Dunedin City Council business development visitor industry adviser Sophie Barker said.
"We just hope it is the last one."
Ms Barker said those in the visitor industry were emailed about the cancellation, but it was hoped a text alert system would be introduced soon.
Port Otago commercial manager Peter Brown said the wind was strong in the morning and forecast to strengthen later in the day, so the captain made the decision to cancel in conjunction with Port Otago pilots.
"It was the master's final call so we are really in their hands."
Cruise ship captains took into account the size of their vessel and the prevailing weather conditions on the day, and "there was no cut-off level above which or below which things will happen".
Up to 88 cruise ship visits were scheduled for Dunedin this season, but to date three had cancelled, including Sun Princess on November 2, and Sea Princess on October 14.
Passengers for all three vessels totalled 5950, while crew totalled 2750.
Taieri Gorge Railway chief executive Murray Bond said the latest cancellation was "extremely disappointing, but understandable given the conditions".
The three cancelled vessels had the largest number of paying passengers scheduled to ride on the train , and the impact could be measured in six figures.
"We have lost tens of thousands of dollars, it is impossible to get that back.
"Already a few months into the financial year and it will be a particularly bad year for Taieri Gorge Railway."
Catered meals from the cancelled trip were donated to several local groups, including Montecillo Veterans Home and Hospital.
Larnach Castle marketing manager Deborah Price said the cancellation was "disappointing but that is how it is; safety first and we understand that".
The notice came early enough to contact staff, and make alternative arrangements for catering.