Fewer puffins are going to breed at the UK's largest colony of the species, on the Isle of May, scientists report.
Numbers are down to about 41,000 breeding pairs this year from almost 70,000 pairs in 2003.
Researchers believe the decline is linked to changes in the North Sea food web, perhaps related to climate change.
Birds are also arriving underweight, which the RSPB describes as "worrying", because puffins are generally able to feed on a range of creatures in winter.
Losing count
The Isle of May, in the Firth of Forth, is home to the UK's largest single puffin colony, although more birds overall nest in the St Kilda archipelago.
Mike Harris, from the Centre for Ecology and Hydrology, has been monitoring and studying the Isle of May population since the 1970s, labelling individual birds with rings to follow their progress.
After decades of spectacular growth, he now believes the colony is in decline.
The five-yearly count of nesting pairs, which Professor Harris's team completed in April, revealed the decline.
"Also, we found some birds were coming back later than expected and others were coming in underweight," he told BBC News.
"And a lot that we knew were alive last year have not turned up at all, so we assume they're dead - although it's possible they knew it was a bad year for food and decided not to come back at all."
The numbers recorded would indicate a population fall of 40%, though because not every single nest can be counted the scientists believe it is more accurate to give a figure of "at least 30%".
Tangled web
Puffins spend the winters at sea, floating, swimming and diving for food, coming to land only during the nesting season.
In the winters they catch fish, squid, worms and other much smaller marine organisms, which means they are more flexible feeders than other seabirds.
"So whatever the problem is, it's got to be a widespread one," said Professor Harris.
The suspicion is that climate change is altering the distribution of plankton across the North Sea.
This disrupts the entire food web, including predators such as puffin.
"This fits in with other evidence that North Sea birds have been desperately short of food over several seasons," said the RSPB's Grahame Madge.
"But these have been birds such as the Arctic tern and kittiwake which only feed in the top part of the sea.
"This is probably the best adapted seabird that the UK has; they're deep divers, they're specialists in going down deep into the water column to find fish, so it's troubling to find that they're encountering a shortage of food."
Richard.Black-INTERNET@bbc.co.uk
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