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Operators have been banned by Port Otago from entering the wharf area to sell products to passengers and crew, in a move consistent with all other New Zealand ports.
Tours and attractions are instead marketed through a marquee staffed by Dunedin i-Site employees.
Some tour operators cited reduced business from loss of the wharf presence and accused i-Site staff of bias towards certain companies.
Such issues will be addressed at the debriefing, to be held near the season's end in late April.
The 2013-14 cruise season from October to May was expected to bring about 148,000 passengers and 65,000 crew to Dunedin on 85 ship visits, and be worth about $32 million to the city.
A tour operator, who asked to remain anonymous, contacted the Otago Daily Times saying i-Site staff were being ''bribed'' by larger companies which paid a higher commission that smaller operators could not match.
But i-Site manager Louise van de Vlierd said a standard 12.5% commission was taken for all bookings, using the same protocol as used at the Dunedin Visitor Centre.
Ms van de Vlierd said operators who thought otherwise could be confused by commission rates charged by cruise ship agents or wholesalers.
They took between 20% and 30% for booking cruise ship passengers on tours, before ships even got to Dunedin, and that had nothing to do with i-Site staff, Ms van de Vlierd said.
''We have to be totally impartial and our main priority is to the customer. If they ask for a certain tour, we can't sell them another to make numbers even,'' she said.
''I would love to be able to fill every single tour every time a cruise ship is in, but it doesn't happen like that and it didn't happen last season, either.''
Data collected at the wharf by a University of Otago student showed about 10% of cruise ship passengers disembarked without a plan for their time in Dunedin.
About 33% arrived having already booked tours through a cruise ship agent, about 40% took shuttles into the city rather than taking tours, and about 10% either did not leave the ship or chose just to walk around Port Chalmers.
About 5% independently booked tours online before arriving in Dunedin, and the remainder disembarked undecided.
Those were the passengers who might previously have been swayed by operators on the wharf, who now asked i-Site staff which tours and attractions would best suit them.
Ms van de Vlierd said previously the first operators to make contact with disembarking passengers got business, but now visitors could consider and evaluate all options displayed inside the marquee, without bias.
Each operator had an A3 poster space and could pay $90 for additional brochure space.
Ms van de Vlierd said tours without a minimum capacity were favoured by passengers.
''If there is a minimum number that have to book for the tour to proceed, passengers will choose another which is definitely going,'' she said.
Dunedin City Council visitor industry business development adviser Sophie Barker said because most passengers planned tours before they arrived, it was vital operators had extensive online marketing.
Businesses which had their own websites, as well as a presence on those of Tourism New Zealand, Tourism Dunedin and TripAdvisor, were the most popular, she said.
Ms Barker said ultimately operators were responsible for their own marketing and promotion, but she was always willing to spend time with those struggling to establish an online presence.
It was a very competitive market, made more so by the increasing number of tour operators, she said.
''There are a lot of operators in Dunedin, about 40 or so, and everyone is competing for a slice of the same pie.''