Curlews, lapwings, oystercatchers and redshank have all decreased in numbers, Scottish Natural Heritage (SNH) found. However, the number of farmland seed-eating birds, such as linnets, skylarks, tree sparrows and yellowhammers, all rose.
Farmland birds in Scotland and further afield have been decreasing since the 1950s, with major declines in the 1970s and into the 1980s.
More intensive farming, climate change and changes in the areas where Scotland's farmland birds spend the winter have all contributed to the fall in numbers, according to SNH.
Susan Davies, the agency's director of policy and advice, said: "Many of our waders are struggling and that action needs to be taken.
"It's not all bad news though, and it's heartening to see some of Scotland's farmland birds increasing. The hard work by farmers and volunteers can pay dividends in helping wildlife.
"There are promising signs that agricultural programmes which supported farmers to, for example, leave set-asides and grass verges uncut are working to help birds like skylarks and sparrows.
"With concerted action, it's possible to improve the fortunes of farmland birds - though clearly there is still a lot to do, particularly for the waders.
"Thanks to the hard work of others, including volunteers and conservation groups, we know what needs to be done to help these birds. Through their efforts, we can measure the success of farmland bird initiatives, and once again have our fields filled with the calls of lapwings and curlew."
The SNH said the trends for farmland seed-eater birds have tended to be more favourable in Scotland in recent years than in England and Wales, where skylarks and yellowhammers have seriously declined.
Phil Harrison, a research fellow at St Andrews University's Centre for Research into Ecological and Environmental Modelling, said: "The Breeding Bird Survey (BBS) data analysed in this report is based on some of the most robust sampling methodology available for monitoring biodiversity on a large scale."