Doc recently finished its pre-fledge nest checks of yellow-eyed penguin populations along the coast from Oamaru to the Catlins.
Doc ranger Mel Young said avian diphtheria caused the death of about half the chicks at Boulder Beach and Sandfly Bay on Otago Peninsula, leaving only 70 chicks to fledge.
Overall there were about 485 nests along the coast which was similar to the previous year, she said.
Most of the eggs hatched, the majority survived to the pre-fledge check and had since fledged slightly earlier than normal, Ms Young said.
Their weights were mostly very good with a weight range of 1.9kg to 7.1kg. A weight of 5kg at fledging is considered optimal for the chicks' survival.
Those significantly lighter than 5kg were removed from the wild and transferred to Penguin Place's penguin hospital to be "fattened up" and to relieve the parents, which needed their strength for the upcoming moult, she said.
Penguin Place's Glen Riley said up to 50 birds had been in the hospital in recent times. Some 30 "patients", mostly younger birds with problems feeding, there at the moment. Ten were released last week.
"There's been a food shortage, with adult birds struggling to raise their chicks."
The aim was to fatten them up to 5.5kg to give them the best chance at survival and the birds had been arriving at the hospital weighing about 3.5kg to 4kg. It took up to six weeks to get them to the required weight, he said.
They were able to do this work thanks to Sanfords in Timaru, which supplied the fish, Mr Riley said. As each bird ate about five fish twice a day, the hospital needed about 500 fish a day.
Yellow Eyed Penguin Trust field manager Dave McFarlane said it had been a "pretty positive" season for the trust's reserves, with average chick weights slightly up on last year and nest numbers on a par with other years.
For the first time all of the chicks on the reserves were microchipped, he said.
Ms Young said most adults seen by Doc were in a good condition which was important for the moulting season when they did not go to sea until they had their new coat.
"The next couple of weeks will be really hard for them. They could turn up on any beach in Otago, which means they could be at risk of being killed by dogs."
The trust and Doc urged anyone who saw a penguin they believed was at risk, sick or dead to contact Doc in the first instance.
