The recommendation comes after a Bryde's whale was found floating in the Gulf last month and an examination showed it was hit by a vessel, most likely while still alive.
The 15m female whale was buried at Calypso Bay.
The New Zealand population of less than 200 of the endangered species is centred on the Hauraki Gulf.
Dr Constantine and fellow researcher Dr Natacha Aguilar attached multi-sensor tags to the whales by suction cup to track their behaviour below the surface of the ocean.
The whales were found to spend most of their time at relatively shallow depths within striking range of ships entering the Hauraki Gulf.
They were very active during the day, staying near the surface and diving less than 10m, and were closer to the surface at night.
"This was a surprise - it's very unusual behaviour for large baleen whales. The pattern of being particularly close to the surface at night time when they're resting, and likely to be less vigilant, makes these whales even more vulnerable to ship strike."
Some 41 Bryde's whales have died in the region in the last 16 years. Of the 18 examined for cause of death, 15 whales were found to have died due to ship-strike, the researchers said.
The results of the study will be used in upcoming discussions with Maritime New Zealand, Ports of Auckland, Department of Conservation and other stakeholders.