The Yellow-Eyed Penguin Trust and the Department of Conservation held a seminar in Dunedin on Thursday to discuss penguin data and what to do in the future.
Trust executive officer Sue Murray said the sample population on the north coast of Stewart Island had halved from 32 pairs to 16 pairs, over nine breeding seasons from 1999.
The trust had started a five-year investigation into the decline of the penguins, in 2003, thinking it was because of feral cat predation.
But the conclusion was completely different - the decline of the breeding pairs was mainly because of starvation and disease, and not because of cats.
Doc southern islands area manager Andy Roberts said it was hard to tell which came first - whether chicks caught a disease and then starved, or whether the chicks starved first and were then killed by disease.
The two diseases caught by the penguins are either leucocytozoon or diptheria stomatitis.
There were thought to be between 1600 and 1700 yellow-eyed penguins in existence, and mainland Stewart Island would have had about 400.
But Mr Roberts said this may have declined to 190 breeding pairs if the disease had been as potent on the rest of the island, as the sample population.
The next step was to conduct a census of the entire population of yellow-eyed penguins on Stewart Island, which would take place over the next year, and to see how badly the population was affected.
But Mrs Murray said the plan depended on the ability to get funding. The trust had already spent $350,000 on research on Stewart Island.
The trust was already committed to other substantial projects, and additional funds would be needed for work to continue on the project.
The trust had two field officers working on the island for six months a year.
Also involved in the study were researchers from the University of Otago, Massey University and the Ministry of Agriculture and Forestry.
There are about 480 yellow-eyed penguins breeding pairs on the Otago coast.
