The awards, given every four years, recognise outstanding international achievements in bird conservation and were presented at the weekend by BirdLife International honorary president Princess Takamado of Japan, at its world conference in Buenos Aires.
Royal Forest and Bird Protection Society of New Zealand general manager Mike Britton, whose organisation nominated the trust for the award, accepted it on the trust's behalf. Ten awards were given.
The Yellow-eyed Penguin Trust has spent the past 20 years helping the endangered penguin, which makes its home along the Otago coast, by purchasing land for natural habitats, fencing and planting, predator control, funding research, advocacy, education and awareness campaigns.
Founding trustee Euan Kennedy said the award was international recognition for the trust's vision and hard work.
"Coming from one of the senior bird conservation agencies it is really something - a real honour."
Over the years, the trust's work had succeeded in "taking the human boot off the throat" of the penguin, helping it avoid calamitous or permanent decline.
The trust had also been successful in making the penguin a symbol of New Zealand conservation: "We've made penguin conservation sexy."
Trust field officer David McFarlane said the penguins would need help for the foreseeable future.
The 2008 breeding season was about to begin, with penguins due in from the sea to nest and lay eggs.
The trust had set up predator traps in its reserves and would now minimise its involvement so the penguins could nest in peace, he said.