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An environmental risk assessment report was commissioned by Environment Canterbury to address residents' concerns over the negative impact cruise ships may be having on the seabed and water quality.
While it found the potential effects can be appropriately managed, it stated the available research is not sufficient to provide a definitive answer.
Now ECan will ask the cruise ship industry to provide an independent scientific study over the next two years.
Said Canterbury regional harbourmaster Jim Dilley: "We believe it will identify exactly what is taking place and will allow us to address any concerns."
The report stated Akaroa Harbour has "very high" ecological values.
It has rare Hector's dolphins, many threatened seabirds, a marine mammal sanctuary and several areas of outstanding or significant natural value.
New Zealand Cruise Association chief executive Kevin O'Sullivan said the report indicates adequate controls are already in place.
About 90 cruise ships visited Akaroa between October 2018 and April this year, up from 75 the previous year.
This number is likely to be reduced once the new Lyttelton cruise ship berth is completed, he said.
Residents said Akaroa is also struggling to cope with the massive influx of visitors. As many as three cruise ships a day can arrive in the harbour.
Akaroa is home to about 600 people, but its population increases by 4000 during the peak of the cruise ship season.