The pattern, first noticed on Otago Peninsula beaches, in particular Sandfly Bay, more than three years ago, is now emerging at other sites along Otago's coast, even in the Catlins, Doc ranger Mel Young says.
Research showed chicks with weights under 5kg had a lower rate of survival.
Their low weight was often the result of not being fed because their parents were staying in the water rather than crossing the beach when humans were present.
While no statistics were available, the trend had become noticeable in the Catlins at an area at Long Point accessed regularly by paua collectors and surfers and at Jacks Bay.
"It's definitely a concern."
Doc had tried to halt the pattern on Otago Peninsula by instituting a range of measures at Sandfly Bay to educate the public to minimise their impact on the birds and by closing Boulder Beach to the public during the breeding season.
The work at Sandfly Bay was paying off, with all eight nests remaining active during the season, she said.
The chicks' mean weight was 5.77kg, compared with the previous year's average of 5.2kg.
"Two chicks and an egg were lost early on, but all remaining 13 chicks not only survived, but were excellent weights."
At Boulder Beach, while chick survival was high, weights "were not fantastic", with an average weight of 5.2kg.
"Surfers still entered the breeding area during the closure, which was disappointing," Ms Young said.
Doc community relations programme manager David Mules said Doc had improved signs and viewing at Sandfly Bay, and for the past three seasons had volunteers on site during the evenings to talk to visitors.
"We're very pleased with the outcome.
"The factors involved are complex, but one significant factor is the great work volunteers are doing to minimise the impact on penguins."
However, despite the good season, Sandfly Bay was still a difficult site to manage, he said.
"If we fail at Sandfly Bay, it does not bode well for other sites along the coast."
Ms Young said overall conditions this summer were favourable for chick rearing, with many pairs of penguins able to raise two chicks to healthy weights.
She put the success of the season down to "good food" being available for the birds this year.
North Otago weights and survival rates were also good and the Yellow-eyed Penguin Trust was pleased with the fledging weights of the penguins on its reserves, although chick numbers were down.
About 420 nests were monitored by Doc throughout the season to determine breeding success and more than 100 chicks were "injected" with microchips to identify them.
"It's really important that the public let Doc know when they see a dead or injured hoiho, even if it doesn't have a band, as it may have a microchip."
