The Finnish-built Voyager carries more than 3100 passengers - among the largest passenger capacities of any vessel calling at New Zealand ports. The other affected vessel, the French-built Pacific Pearl, carries more than 1600 passengers.
This is believed to be the largest loss of cruise passenger visits to Dunedin on a single day in recent years.
Voyager, which had been due to dock about 6.30am yesterday, waited off the Otago heads for more than five hours, hoping for a break in the weather.
But after high winds continued within the harbour, the vessel then left for its planned visit to Fiordland.
And Pacific Pearl, due to arrive at 7am, headed for its next port, Akaroa.
Four cruise ship visits to Dunedin had to be called off last cruise ship season, Dunedin City Council officials said.
And high winds elsewhere in the country stopped Sea Princess, which carries about 1900 passengers, becoming the first cruise ship of the season to visit Dunedin, on October 16.
Port Otago Ltd commercial manager Peter Brown said yesterday's outcome had been ''disappointing for all the operators'', including Port Otago, but the reality was that this was ultimately a ''safety matter'' and safety had to come first.
''We just have to accept that.''
Council officials said business amounting to hundreds of thousands of dollars had been lost yesterday, but it was necessary to be philosophical and many other opportunities lay ahead throughout the cruise season.
Spirit of Enderby is due to arrive in Dunedin today.
The vessel, with 48 passengers and 24 crew, is expected to berth at 6.30am and will sail at 10am tomorrow.
