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It follows a summer in which the nest count dropped to 225 from last year's 260, continuing the species' decline on the mainland.
The chicks were taken to the Dunedin Wildlife Hospital late last month, after fears they would starve.
The young birds, 11 of which were from the Catlins, are now recovering at Penguin Place, in Harington Point.
Penguin Place manager Lisa King said the chicks were now doing ''extremely well''.
''They're putting on weight rapidly.
''Most of them have put on a kilo since they came here.
''They'll be here for another month or so.''
Yellow-eyed Penguin Trust general manager Sue Murray said it only ever uplifted chicks if they were deemed unlikely to survive.
''So that's when they are less than 60% of body weight.
''They'll get supplementary feeding to give them the best chance of survival.''
The trust's theory on the chicks' plight was that flooding last November affected some sites, making seas murky and more difficult for the animals to find food.
''It was really soon after the chicks hatched. Penguins are very visual hunters.''
The trust also noticed other ''unusual things'' this season, including two birds at nests for long periods of time.
''It means one wasn't away feeding.''
Adults were also taking longer foraging trips and returning days later instead of the same day.