The Yellow-eyed Penguin Trust this week presented a report to the Otago Regional Council which showed mass starvation events and large death numbers in the mainland population for 2018-19.
At the start of last season 227 nests were counted on mainland New Zealand, which includes Stewart Island and Whenua Hou/Codfish Island, down from 261 two years earlier.
Throughout that season there were 106 observed deaths, up on 52 the previous season.
This included 63 adults, more than 10 of which were breeding females.
Twenty of these were attributed to avian malaria and the others to a range of causes including starvation and lung infections.
Largely because of starvation, more than 430 birds required rehabilitation throughout the season, 324 of which were treated in Dunedin at facilities such as Penguin Place and the Dunedin Wildlife Hospital.
Trust conservation science adviser Trudi Webster said it was not known how large the mainland population was, but a guess was between 700 and 800.
Some of the increase in starvation among the species could be related to heavy rain and flooding last year from November 17 to 23, which coincided with chick hatching and could have limited visibility while the animals tried to hunt.
The changing marine environment and impact of fishing was likely to have had an impact, Dr Webster said.
"While it's negative, at least people have acknowledged the problem and are doing something about it."
The trust hired another staff member, based mainly in the Catlins, as the season presented "a lot more work on the ground".
It also created an avian malaria action plan which included how to monitor and attempt to control mosquitoes.
This comes after University of Otago researcher Thomas Mattern estimated the species could be functionally extinct from the mainland, meaning the population could not sustain itself without major intervention, any time from 10 years onwards.
