A new report from Scottish Natural Heritage (SNH) shows that 87 beavers were shot in the Tayside region, where an unauthorised population has been spreading over the past decade and causing damage to important agricultural land.
As well as the killings, a further 15 of the creatures were trapped and moved to other sites under the permits.
A total of 83 beaver dams were also destroyed.
Beavers were once widespread in Scotland but were hunted to extinction in the 16th century.
In May last year the animals were officially recognised as a native species and given protection following a successful reintroduction trial carried out in Argyll.
However, a separate population in Tayside - believed to have stemmed from animals that were illegally released or escaped from captivity - has been increasing in the past decade and causing conflict with local farmers, who have suffered losses associated with damage to trees and flooding of fields and crops.
A number of the animals, including pregnant females, have been found unlawfully killed.
Robbie Kernahan, director of sustainable growth at SNH, said: “It’s always been clear to both us and our partners that lethal control of beavers will sometimes be necessary under licence as a last resort when other mitigation is unlikely to be effective.
“Some of the well-documented and most serious issues have occurred on the most productive areas of agricultural land in Scotland.
“Due to their generally being well-drained, low-lying and flat, these areas are often vulnerable to beaver burrowing and dam-building.
“As we work with farmers to trial new and innovative measures for reducing the impacts of beavers on this type of ground, we hope to see less need for control measures in the coming years.
“We also expect to see the beaver population expanding away from high conflict areas and into suitable habitat where beavers can thrive and bring the positive benefits we want to see.”
But naturalists have said the figures are “alarming” and could threaten the continued survival of the species in Scotland.
Sarah Robinson, director of conservation at the Scottish Wildlife Trust, said: “This report confirms that at least one-fifth of the beaver population in Tayside has been shot in a single season.
“It demonstrates that heavy localised culling can impact the population over a wider area, and is halting the ability of animals to spread out through a vacuum effect.
“These are alarming figures. Such a heavy cull has almost certainly had a negative impact on the conservation status of a protected species.
“If lethal control continues at this level, we would have grave concerns for the future of beavers in Scotland.”
Meanwhile, farming leaders have welcomed the licensing system for managing beavers as “effective and fit for purpose”.
“It has allowed the management of beavers in those areas of productive farmland where the species has had a clear impact,” said NFU Scotland president Andrew McCornick.
“The number of beavers and their range continues to expand and it remains vitally important that, where there is conflict, the impact on farmland of beavers in new and existing catchments can continue to be managed through this framework.
“While that may involve lethal control, we note from the report that three-quarters of licence holders have proactively engaged with the role of trapping.”
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