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Tourism operators are questioning whether their presence in Doubtful Sound is putting the area's unique community of bottlenose dolphins at risk.
The industry is facing restrictions, including possible bans on where they can operate, after a Department of Conservation report said the dolphins were "highly likely" to be extinct by 2050.
The report, issued this week, identified boat interactions as the key cause of the declining population.
An interaction is defined as coming within 400 metres of dolphins.
The number of bottlenose dolphins in Doubtful Sound had fallen from 69 in 1994 to 56 last year.
"This decline is one of the steepest ever recorded for a dolphin population that is not exposed to direct or indirect takes from fishing," the report said.
It is based on research by Otago University marine ecologist David Lusseau, who found that dolphins dived for longer when trying to avoid boats.
Research in Shark Bay, Australia, found that the energy expended while avoiding boats made female dolphins half as likely to reproduce successfully as those that were not exposed to boats.
But tourism operators questioned the cause of the decline. Dave Hawkey, chief executive of Real Journeys, the biggest operator in the area, said his company's boats interacted with the dolphins for 12 minutes a day.
"If there are things we can do as operators - creating boat lanes or no-go areas - we're happy to sit down with DOC and work through these issues."
Reg Calder, of Adventure Kayak and Cruise, said other causes such as the dumping of fresh water into the area from the Manapouri power station should be looked at.
But DoC community relations manager Martin Rodd said the department had found nothing that countered the research.
