Sea eagles, buzzards, red kites and hen harriers are being killed by landowners protecting their livestock, the RSPB said.
The bird charity conducted a year-long study into wildlife crimes such as poisoning and shooting involving birds of prey.
The RSPB found 28 cases in which pesticides were used to illegally kill or threaten birds of prey in 2008.
Another four cases involved the discovery of pesticides suspected to be used for illegal purposes, and 42 poisoned baits, also illegal, were found in the Scottish countryside.
One sea eagle, two red kites, 14 buzzards and three ravens were all found poisoned.
Five buzzards and a red kite were found shot, and peregrines and hen harriers disappeared in circumstances that "strongly suggested human interference", the report said.
The cases were reported to the RSPB and the police, and were all confirmed by post-mortems and toxicology tests carried out by Scottish Government agencies the Science and Advice for Scottish Agriculture and the Veterinary Laboratory Agency.
The killings were concentrated around so-called hotspots on the east coast, where much of the land is given over to grouse and pheasants.
RSPB Scotland's head of investigations, Bob Elliot, said: "For a long, long time most birds of prey were seen as a threat to livestock as well as to game birds like pheasant and grouse.
"The killings we found were concentrated in uplands areas, where there are large heather moorlands and areas where there is intensive pheasant rearing.
"It suggests that people are killing predators to protect their stocks."
But recorded cases from the past year may be a fraction of the crimes being committed against birds of prey in Scotland, according to the RSPB.
The report went on: "Given the fact that many of these incidents take place in remote areas, where it is easy to conceal the evidence, it is likely these confirmed cases will undoubtedly represent a tiny fraction of the crimes perpetrated against some of our most highly protected and admired birds of prey."
The charity's head of species and land management, Duncan Orr-Ewing, said: "We know that illegal killing of birds of prey is having a serious impact on the populations of iconic species such as golden eagles and hen harriers.
"We welcome the broad consensus that has emerged from responsible landowners, as well as conservation bodies, that such illegal practices are unacceptable and damaging not only to bird of prey populations but also to the economy of Scotland and our international reputation.
"Birds of prey are national assets, with huge public, cultural and tourism appeal."
Environment Secretary Richard Lochhead said the charity's findings are "shameful".
He said: "Even one incident of deliberate, illegal poisoning would be one too many.
"It is shameful that some of our most iconic species continue to face illegal persecution.
"We will continue working closely with RSPB Scotland and other organisations involved in the Partnership for Action Against Wildlife Crime in Scotland to tackle this threat.
"The illegal persecution of Scotland's bird life is unacceptable, tarnishes our reputation and must be stopped."
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