Of the 30 kororā broughtto Waiheke Native Bird Rescue this summer, just four have survived.
Founder Karen Saunders said all penguins found in the Hauraki Gulf this year have been severely emaciated.
"Most of them died in transport to us and if they didn't die on the way, they died shortly after arrival or the injuries were so severe we had to euthanise them."
All the chicks in nesting boxes in the area were found dead.
Emaciated little blue penguin population struggling to survive - watch on TVNZ+
Three of the surviving fledglings will be released in the next few weeks. The fourth, known as "Bangers", was in critical care, being fed anchovies multiple times a day to stablise his weight, after arriving extremely malnourished.
Warming sea temperatures are understood to be a major factor.
MetService oceanographer and general manager of research Brett Beamsley said marine heat waves are increasing.
"The intensities are increasing as well... but also the duration. So we're having very, very long marine heat waves."
Fish kororā usually catch close to shore are migrating into cooler deeper waters, which means the search for food is becoming more dangerous.
Of the 12 penguins treated at Auckland Zoo since January only a few have survived. A female suffered a permanent injury to her flipper which means she is unable to be released and the zoo is now her home.
Penguins brought in from the Hauraki Gulf area have been shrinking over the years. Vet Dr James Chatterton said they are now half the weight they should be.
"Their chances will get better if we can undo some of the damage that's been done to the hauraki gulf and also if we can all work together to try and combat climate change and warming oceans."
Work is underway with help of the Hauraki Gulf Marine Protection Act.
Executive officer of the Hauraki Gulf Forum Beth Rose said the group has been advocating on major issues for years.
"Some really key areas are over-fishing, removing those destructive fishing practices from the marine park.
"Marine protection, we've got a little bit of that last year and that lifted us off quite a low base but we'd like to see more of that."
The Hauraki Gulf Forum will have a quarterly meeting to discuss progress and ongoing work at the end of this month.
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