Environment Minister Paul Wheelhouse strongly condemned those who seek to kill the animals and said some of Scotland's magnificent wildlife was being put at risk.
Scottish Natural Heritage will now examine if general licences for trapping and shooting wild birds could be restricted on land where there is good reason to believe crimes have taken place.
An examination of whether legal penalties imposed on those who commit wildlife crimes are tough enough will now be carried out.
Meanwhile, Lord Advocate Frank Mulholland has ordered prosecutors in the wildlife and environmental crime unit to work with Police Scotland to ensure all investigative means possible are being used.
Mr Wheelhouse said: "I am determined to stop illegal persecution of raptors that continues to blight the Scottish countryside.
"These outdated, barbaric and criminal practices put at risk some of our most magnificent wildlife and have horrified a wide range of people across Scotland and those who love Scotland."
He added: "Wildlife crime, and raptor persecution in particular, often takes place in remote locations or in the dark of night. By its very surreptitious nature, the likelihood of being seen by a member of the public who can report the matter to the authorities is small. Through these new measures, I am keen to maximise the opportunity for offences to be detected and offenders to be tracked down."
Mr Wheelhouse said that eradicating crimes against birds of prey remains a high priority for me and for this Government.
He stated: "It is not, however, the sole responsibility of government. Law enforcement clearly has a key role to play. Also, everyone should make clear their disapproval to the minority whose actions are tarnishing the reputation of Scotland's country sports."
Duncan Orr-Ewing, head of species and land management at RSPB Scotland, praised the strong leadership on the issue.
He said: "It is firmly established that the prevailing levels of human killing are having a devastating effect on the populations of some of our native bird of prey species, including golden eagle, hen harrier and red kite.
"Recent incidents involving the killing of golden eagles and other birds of prey species have rightly caused public outrage.
"We welcome the clear leadership shown today by the Scottish Government indicating these crimes will not be tolerated in modern Scotland.
"We support further sanctions to act as a deterrent and to make it easier for the authorities to convict those involved. We hope these measures will be implemented soon and are well targeted to bear down on the organised crime behind much of this activity."
However, the Scottish Land Estates organisation voiced fears the Government could be moving away from a criminal standard of proof in wildlife crime cases.
Chief executive Douglas McAdam stressed it unreservedly condemned wildlife crime, adding that people convicted of such offences should face the full weight of the law.
He said restricting licences on land where crimes are believed to have taken place, would "demand a very robust evidence base".
Mr McAdam said: "If the Scottish Government intends to move away from a criminal standard of proof in wildlife crime cases, then this is a very serious move and deeply concerning for all land managers, especially as this may result in unfair restrictions on people's livelihoods. The detail of any such proposals will be crucial."
Mr Orr-Ewing claimed that, while many Scottish sporting estates had "a good reputation for giving a home to our native bird of prey species, the recent and historic problem of the killing of protected raptors is largely associated with land managed for commercial driven grouse shooting".
He said: "This sector appears unwilling in many cases to embrace the change in public expectations, as well as adopting modern sustainable land management practices, with the protection of golden eagles and other birds of prey a key test of their positive intention."
Police Scotland and RSPB Scotland have appealed for information after a protected red kite was found dead in woodland near Aboyne in Aberdeenshire in April. A post-mortem examinationconfirmed its death was not by natural causes. Poisoning incidents fell from 10, involving 16 birds, in 2011 to three in 2012, according to the latest figures.