RSPB Scotland said 20 birds were deliberately poisoned in 17 separate incidents last year, including a golden eagle, four red kites and seven buzzards.
The report said many of the animals died after ingesting bait laced with highly toxic chemicals.
The charity said while the number of detected poisoning incidents has fallen in comparison to recent years, there is still a "significant threat" to Scotland's birds of prey.
There were 16 other incidents recorded during 2011, including a buzzard which starved to death in a crow trap, the destruction of a goshawk's nest, as well as a short-eared owl, two peregrines and three buzzards being found shot.
Most of the illegal killings are said to have taken place in the eastern and central Highlands and southern Uplands, in areas which are managed for driven grouse shooting.
Ian Thomson, head of investigations at RSPB Scotland, said: "Many of these crimes were discovered purely by chance, by walkers or birdwatchers. It's safe to assume that many victims of illegal killing are not detected or reported. While there may be some indications that the indiscriminate use of illegal poisons is on the wane, it is clear from this report there is a long way to go before these crimes are eradicated."
Duncan Orr-Ewing, the charity's head of species and land management, said: "These crimes can have a devastating impact on the population of rare and slow- breeding species."
l Police have appealed for information after a Hen Harrier was shot dead in Fettercairn, Aberdeenshire, last month.