Sue Reed-Thomas, DoC's director of operations for the northern North Island, said the Bay's bottlenose dolphins were in a unique situation because they lived in a boating Mecca. The study found the dolphins were spending 86 per cent of daylight hours in the presence of at least one boat.
"This is very disruptive for the dolphins. It means they spend far less time feeding, nursing their young and sleeping," she said.
"We know people love dolphins. People are simply loving them too much."
Lead researcher Catherine Peters, of Massey's Coastal-Marine Research Group, said both commercial and private vessels were altering dolphin behaviours critical to their survival.
The study found when boats were within 300m dolphins spent significantly less time feeding and resting, and more time engaged in energy-sapping activities such as socialising and diving.
While the link between the dolphin's changed behaviour and falling population could not be proven, it was clear their decline was accelerating and intervention was needed.
Ms Reed-Thomas said DoC was working with boat owners, iwi and the community to improve the way interactions between boats and bottlenose dolphins were managed.
DoC was developing an education and engagement programme, was looking at strengthening marine mammal regulations, and would extend its moratorium on new dolphin-watching operations in the Bay. The moratorium had been due to expire in June.
Everyone who took a boat on the water in the Bay needed to be aware of the problem so they could play their part in protecting the dolphins - though it was difficult to manage a group of freely swimming animals, she said.
"The dolphins often swim towards boats themselves and you simply can't put a barrier around them or monitor every interaction they have."
Current restrictions limit the number of boats that can interact with a group of dolphins at any one time and prohibit swimming with dolphins when calves are present. They also set speed limits around dolphins, a "lunch break" when the mammals are supposed to be left alone, and no-go areas such as Deep Water Cove.
The only companies currently licensed to run dolphin-watching cruises in the Bay are Fullers GreatSights, Explore and Carino Sailing.
Fullers GreatSights manager Charles Parker said his company was committed to working with DoC, other licensed operators and the community to ensure a sustainable bottlenose dolphin population and develop a new set of rules protecting all marine mammals.
"Over the past 18 months we've made voluntary reductions in our level of interaction with marine mammals. Our skippers and crew are passionate wildlife advocates and feel privileged to be able to interact with dolphins and other marine mammals in accordance with the regulations," he said.
Last summer DoC Bay of Islands boss Rolien Elliot said she was "generally happy" with the behaviour of licenced operators but had serious concerns about boaties who had been seen travelling at speed through pods of dolphins. Local boaties generally knew the rules but some visitors claimed ignorance.
Bottlenose dolphins are found worldwide but are classified as endangered in New Zealand because their three main populations - in the Bay of Islands, Fiordland and northwest of the South Island - are small. The total New Zealand population is thought to be around 1000.
The Massey University study took three years to complete.
- Call 0800 DOC HOT (0800 362 468) to report any marine mammal which is being harassed, is badly injured or entangled.
