The Herald understands 20 were already dead when DoC staff arrived, due to fighting and the stress of being in close confines with other birds.
Officials repackaged the surviving birds into better containers and offloaded them for transport to Green Bay Bird Rescue Centre, where they were tube-fed and kept temporarily.
Thirty-seven Buller's shearwaters were released at night by DoC, Green Bay Bird Rescue and SPCA staff from Castor Bay cliffs facing the sea, away from lights and main roads.
DoC Auckland biodiversity supervisor Dr Art Polkanov said all of the birds successfully flew away, while the bodies of those that hadn't survived were taken by Auckland Museum staff to support ongoing research.
DoC would be working with Ports of Auckland to get information out to vessels on how to handle seabirds that land on ships, he said.
While DoC sometimes received exhausted birds such as albatrosses and petrels from container ships, it was unusual to get birds from a cruise ship.
"As a rule, if birds are uninjured, the crew are encouraged to release them over the side of the ship," he said.
"If the birds are not well or crew are not familiar with seabirds and not sure if they are able to take off from water surface, it would be better to place them in individual boxes and take ashore for examination, possibly treatment and release in a safe environment."
Buller's shearwaters breed only on Poor Knights Islands, while colonies of the "nationally vulnerable" flesh-footed shearwater in the Hauraki Gulf are found at the Hen and Chickens Islands.
More Shearwater photos. Each bird was given a health assessment, weighed, and tube fed on arrival. Pools were put in...
Posted by New Zealand Bird Rescue Charitable Trust on Friday, 18 May 2018
Forest and Bird seabird advocate Karen Baird said the case was "heart-breaking".
Seabirds being attracted to lit-up vessels as they passed by their habitats was a "potentially huge" problem.
"Most vessels travelling down our north-east coast at the time of the year when these birds are fledging will potentially end up with birds on board at night.
"Young seabirds, especially, were vulnerable to light attraction, as they hadn't learned how to avoid it yet, she said.
"Most of these birds will have just fledged from the colony I was working on a few weeks ago, which is very sad."
Baird said the North Island's north-east coast had already been identified as a globally important site for seabirds through BirdLife International's Important Bird Areas programme.
She argued that DoC should develop best-practice advice so that all vessels travelling into Auckland were aware of the problem.
"This is a potentially major unknown source of mortality which will only get worse as shipping traffic increases into Auckland and needs immediate addressing."