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The trust, which is in its 28th year, has traditionally focused its work on increasing penguin numbers by protecting them and their habitats on land.
However, it was becoming increasingly apparent that what happened to the penguins at sea needed to be better understood, trust general manager Sue Murray said.
''It's a big turning point in penguin conservation.''
This had been reinforced by mass mortality in 2013 and starvation problems this summer.
Combined, the two events had resulted in nest numbers halving at the trust's Otago Peninsula colonies - Okia Reserve dropped from 13 to 5 and Otapahi ffrom 19 to 5.
Like every non-profit organisation, the Yellow-eyed Penguin Trust was struggling for funds, although it had strong support from many sectors thanks to having a charismatic bird people loved, she said.
''The challenge is we've expanded so much that we have a constant requirement for resources.''
The issue was highlighted by trust chairman Eric Shelton in his report to this week's annual meeting.
''This coming financial year will be challenging and will require making some difficult strategic decisions involving the allocation of resources,'' Mr Shelton said.
Mrs Murray said while the past nearly three decades' work meant those involved in penguin conservation had a good understanding of the penguins' biology, breeding and habitat, much was not known about the marine environment where they sourced their food.
Finding out why so few returned to Otago's shores after fledging was just one question which needed answering, she said.
Getting a better understanding of that environment required costly research and monitoring. How that fitted in with the trust's core work needed to be considered.
''They are so much more difficult to resource.''
This year, the trust would be considering how to advance ''in-house'' science to help guide its work in the future.
''Maybe we need to fund research.''
The trust had also commissioned Wildland Consulting to review its work on Stewart Island and help guide its future work there, given resource limitations.
• For the first time, the Yellow-eyed Penguin Trust has its full complement of 15 trustees. At this week's annual meeting, Murray Brass and David Smith were elected to the board for the first time, while Lala Frazer and Mike Morrison were re-elected.
They joined the trustees co-opted last year, Nigel Stirling, Jesse James and Luke Gardener, and existing members chairman Eric Shelton, Margaret Munell, Euan Kennedy, Linda Reynolds, Pat Mark, Peter Simkins, Hoani Langsbury and Tim Mepham.