Seven incidents of deliberate poisoning were recorded, down from 17 the year before, wildlife charity RSPB Scotland said.
A golden eagle, two buzzards, two cats and a raven died after eating bait laced with highly toxic and banned pesticides.
Poison bait was discovered in a seventh case but no victim detected.
The charity welcomed the drop but warned about the illegal killing of birds of prey by other means, with 13 further incidents also recorded. These include the shootings of two golden eagles, a hen harrier, a goshawk nest and a short-eared owl.
Another golden eagle, two buzzards and a peregrine falcon were caught in illegally set spring traps. Two goshawks, a tawny owl and a buzzard died in illegally operated crow traps.
A further 27 probable incidents were identified in the charity's annual report, including cases where satellite-tagged birds disappeared without explanation.
Stuart Housden, RSPB Scotland director said "We applaud the continued focus on tackling raptor persecution by the Scottish Government, but much remains to be done.
"We also welcome the decline in illegal poisoning. However, if those who wish harm to our country's birds of prey simply turn to other forms of persecution, such as shooting or trapping, then there is little to celebrate.
"The deaths of these golden eagles are particularly appalling, given that the golden eagle was recently voted the nation's favourite species in the SNH poll for the Year of Natural Scotland."
He called for a review of how the law is applied in cases of birds of prey. The majority of reported or suspected incidents were in areas managed for driven grouse shooting in the eastern and central Highlands and the southern uplands, the charity said.
Douglas McAdam, chief executive of Scottish Land & Estates, said the substantial progress being made in tackling wildlife crime reflects the efforts of organisations such as the Scottish Government police, landowners, gamekeepers, land managers and charities such as RSPB working together through the Partnership for Action Against Wildlife Crime.
He said: "It is right the RSPB report highlights the unacceptability of wildlife crime but we believe it would be more productive if the charity focused more on promoting what can be achieved in tackling the issue rather than trying to point fingers. The implication that this is always the fault of shooting interests is simply not borne out by the evidence."