The new figures from the Royal Society for the Protection of Birds have sparked fresh fears over the future of the elusive dotterel, which winters in Africa and comes back to Scotland in April and May.
Almost two-thirds of the UK's dotterel population are found in the Cairngorms but the estimated number of dotterels in the UK has fallen from 630 breeding males in 1999 to 423 breeding males in 2011.
The change continues a longer-term decline since the first survey in 1987/88, when 981 breeding males were estimated.
Scientists say more research is needed to establish what might be causing the decline, and whether climate change could be having an effect on their habitat and food sources.
Mark Eaton of RSPB said: "Scotland's Highlands provide an important home for dotterel and the presence of the species offers a good indicator of the health of our montane landscapes.
"To see such a significant drop in their numbers over the past three decades is deeply concerning.
"We are now embarking on research in partnership with Aberdeen University and SNH to examine possible causes of these declines, from climate change to grazing impacts and the effects of atmospheric pollution on sensitive mountain-top vegetation."
The decline of the dotterel is one of the changes in Scotland's bird populations highlighted in the latest State of the UK's Birds report. The report has been compiled by scientists from the RSPB, Scottish Natural Heritage (SNH) and Natural Research.
Published today, it also reveals severe losses of farmland birds such as grey partridge, lapwing and corn bunting.
Eileen Stuart, SNH Head of Policy and Advice, said: "The declining numbers of some birds, particularly the drop in dotterels, is obviously very worrying, although it was good to see that a few birds, such as red kites, goldfinch and the blackcap, are doing well."
She said some species were particularly vulnerable to international factors, such as climate change and fishery policies. But she added that SNH was committed to maintaining good-quality feeding and breeding areas in Scotland to give them the best chance of survival. "Farmland birds continue to face difficult challenges, as do some of our more well-known woodland and garden birds", she added.
The report examined the UK's 107 most widespread and common breeding birds and found that 16 of those species had declined by more than one-third since 1995.
These included the cuckoo, starling, lapwing, whinchat and wood warbler. The RSPB said it was particularly worried about the populations of the turtle dove, found south of the border, and the grey partridge, which have halved since 1995.
Numbers of yellow wagtails, whose global population is found almost entirely within the UK, have fallen by 45% since the same date.
Meanwhile Colette Hall, species monitoring officer with the Wildfowl and Wetlands Trust, said: "There's worrying evidence here that the breeding ranges of many of our waders are drastically shrinking.
"We're losing much-loved species like snipe or lapwing completely from parts of lowland Britain.
"A main cause seems to be loss of habitat due to wetlands being drained for farming or development.
"We need to protect and restore these habitats in order for species like these - and all wetland wildlife - to survive and prosper."
The RSPB said news of the decline in bird species coincided with the launch of the Bird Atlas 2007-11 published by the British Trust for Ornithology (BTO) last month. It covers all of the UK's breeding and wintering birds and showed the speed at which countryside birds are vanishing across the UK.