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The organisation cared for two penguin colonies at Moeraki, where there were 38 nests producing 49 living chicks.
Twenty-five were big enough and old enough to be released.
Penguin Rescue manager Rosalie Goldsworthy said the hand-raised chicks had been moved to a pen on the foreshore with the doors open.
The chicks had been fed once a day for a week in the pen and were now free to go — or stay, if that was their preference.
"We’re waiting for their instincts to kick in — they’re familiarising themselves with the environment."
A sense of relief was felt by those involved in the penguins’ release.
"I’m very proud of what we’ve achieved this year.
"Despite trials and tribulations, we’ve saved 48 penguins."
Mrs Goldsworthy urged people to be vigilant about keeping their dogs on leads while on beaches for the next three months.
"At this time of year, chicks are fledging and dogs are still the biggest predators of penguins."
There were 155 nests across New Zealand this season, down from 226 nests last year.
Disease, animals such as ferrets and dogs, human disturbance and a loss of habitat were constant threats to the bird.
In late December, three penguins from nests at Moeraki were killed, prompting Penguin Rescue to take 48 chicks into care.