Landowners and managers suspected of wildlife crime could lose licences to trap or shoot birds on their land.
General licences that allow people to carry out otherwise illegal acts, such as controlling certain bird species to protect crops or livestock, can now be be withdrawn under new measures to tackle raptor persecution.
Scottish Natural Heritage (SNH) said the restriction of licences would be made "on the basis of strong evidence" from police and on a civil, rather than criminal, standard of proof.
Environment and climate change minister Paul Wheelhouse said the illegal persecution of birds of prey was "totally unacceptable and barbaric".
He said: "I am both angry and very frustrated that a criminal minority continues to kill and persecute these magnificent birds for their own selfish ends.
"It is too often the case that there is clear evidence that a crime has been committed but the perpetrator is able to hide behind a wall of silence among those who really should be co-operating with the police.
"That is why I asked SNH to consider how better use can be made of general licenses which, rather than a 'right', are a privilege that can and should be withdrawn where there is evidence of illegal activity taking place.
"I am confident these new measures will be a powerful new weapon in our armoury in the fight against those perpetrating raptor persecution in Scotland and hopefully will deter those who might be tempted to commit such a selfish criminal act that stains Scotland's reputation and potentially damage the rural economy."
SNH chairman Ian Ross said raptor persecution damages the £1.4 billion a year value of nature tourism to Scotland's economy.
He said: "We're committed to taking action whenever there is evidence of wildlife crime and we believe this new measure will make it much tougher for those committing offences.
"Because of the remote locations where most wildlife crime takes place, it's often difficult to prove. So, we need every tool we can to fight against those who persecute raptors in Scotland."
Under the plans, general licences will be removed for three years, with possible extensions if evidence of further crime is discovered.
Welcoming the measure, Duncan Orr-Ewing, head of species and land management at RSPB Scotland, said: "Wildlife crime remains a serious problem in parts of Scotland impacting the populations of iconic species including golden eagle and hen harrier.
"This activity has serious implications for the reputation of Scotland as a place that values its wildlife.
"We believe that SNH will have the widespread support of the Scottish public in using these powers and equally no law-abiding landowner should have anything to fear.
"We will judge the impact of this measure by the performance of the populations of key indicator species such as hen harrier, which remains absent due to human killing from most driven grouse moors in the central and eastern Highlands and Southern Uplands."
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