More than 20 beavers have been shot and killed in Tayside, despite landowners being asked to tolerate the animals until a decision has been made on their reintroduction.
Farmers and estate owners have long complained of the damage the beavers are causing in Tayside, particularly through the construction of dams.
A wild beaver population now more than 150 has been growing in Tayside for a decade.
Thought to originate from escapes or illegal releases from private collections, they have been found in waterways from Kinloch Rannoch, Kenmore and Crieff in the west to Forfar, Perth and Bridge of Earn in the east.
A licence is not needed to shoot beavers because they have no legal protection in the UK but possessing and moving a dead beaver is not legal without a licence.
Scottish Natural Heritage (SNH) has licensed the Royal Zoological Society of Scotland (RZSS) to collect any beaver carcases from Tayside and examine them.
SNH’s Tayside and Grampian unit manager David Bale said: “We don’t encourage lethal control. Instead we advocate solutions such as protecting trees and discouraging dam building.
“Removing a beaver simply leaves the territory open for another beaver to move in, so shooting tends to be a short-term solution.”
The UK is one of only seven European countries with no officially-sanctioned wild beaver population.
An official scientific trial saw 16 animals introduced into Knapdale Forest in Argyll between 2009 and 2011, then monitored by scientists.
In June SNH submitted its Beavers in Scotland report on Knapdale to the Scottish Government, which is considering an official reintroduction programme.
The NFU Scotland said farmers fear the impact beavers can have on productive farmland reliant on complex drainage systems. The costs of removing dams and pipe blockages and repairing flood defences was already significant in Tayside, a spokesman said.
When the Scottish Government established the Tayside Beaver Study Group in 2012 landowners were asked to tolerate them, until a decision on the future of beavers in Scotland was made.
But the RZSS has confirmed that, since the end of 2012, 23 beavers from Tayside have been examined 21 were shot and two were killed on the roads.
A Scottish Government spokeswoman said: “We are aware that farmers on Tayside are experiencing issues with beavers and would encourage land managers to consult with SNH on mitigation measures.”