Numbers of kestrel, lapwing and curlew plummeted by between a quarter and almost half between 1994 and 2005 while oystercatcher numbers fell by 22 per cent and the meadow pipit saw a drop of 18 per cent.
All five birds are on the "amber" warning list because of fears that their populations will decline further in future.
The Breeding Bird Survey, which is administered by the British Trust for Ornithology (BTO), also saw the number of swifts fall by 34 per cent and hooded crows drop by 37 per cent, although their decline has not been over a long enough period to put them on a warning list.
The survey was compiled by volunteers who identified more than 70,000 individual birds of 166 species across Scotland in 2005.
Ornithologists say declines in the "specialist" Scottish birds like the meadow pipit and hooded crow could be down to climate change as populations shift north.
The survey found that the struggling species are mainly from upland and moorland areas while those which are increasing are from lower and wooded regions.
Graham Appleton, of the BTO, said: "Many birds in Scotland are doing very well compared to the rest of the UK.
"Blackcap populations are growing because they are moving north from England while some specialist Scottish breeds are declining because they in turn are shifting further north. It suggests that the populations are being affected by the climate."
The survey found the situation in Scotland is better than the rest of the UK where a number of "red-listed" birds are in decline.
The findings show a significant increase in 23 species north of the Border with none declining by more than 50 per cent.
Increases of more than 50 per cent were recorded for grey heron, buzzard, snipe, house martin, wren, mistle thrush, whitethroat, blackcap, goldcrest, great tit and goldfinch.
Across the UK, the biggest loser of the 20th century was the red-backed shrike, the so-called "butcher bird", which was once commonplace but became extinct by 1990.
Highs and lows
Species in Scotland showing a significant decrease from 1994 to 2005:
Hooded crow -37%
Meadow pipit -18%
Species with a "high conservation priority", which saw an increase in the same period:
House sparrow +47%
Linnet +31 %
Song thrush +26%
Less-threatened species seeing significant increases included: