All 87 beavers shot legally in Scotland last year were killed in Tayside.
The figures are contained in a report to the Scottish Government by Scottish Natural Heritage (SNH) this week.
The Scottish Wildlife Trust (SWT) said the killings, carried out with 16 licences, amounted to one in five of Tayside’s wild beaver population and raised concerns about the species’ future prospects.
An SNH survey carried out in 2017/18 suggested there were around 433 beavers in Tayside.
More than half, 49, were killed in territories along the River Isla’s catchment area, 22 in the River Tay’s catchment area and a further 22 around the River Earn.
A total of 83 dams built by the animals, which have European protected status, were removed.
The spread of the beaver population in Tayside coincided with an official reintroduction programme on the west coast, which started in 2009. The animals were hunted to extinction in the 16th Century. The Tay population has grown rapidly from animals which were either escaped or released illegally from captivity and their arrival has led to conflict with farmers and other landowners.
SNH said 60% of the licences it issued which permitted lethal control were not used for that purpose.
The agency received 67 requests for licences in relation to the activities of beavers in 2019, two thirds of which were granted.
No beavers were shot in the Forth Valley area or Argyll.
The SNH report said: “Licensed control has almost exclusively been restricted to farms on prime agricultural land.
“We are still learning how to live alongside [beavers] and how to maximise the benefits they will bring whilst having a proportionate and balanced approach to managing the situations where they may have impacts on other public interests.”
The Scottish Wildlife Trust said lethal control should only ever be used as a last resort.
Sarah Robinson, the charity’s director of conservation, said: “This report confirms that at least one-fifth of the beaver population in Tayside has been shot in a single season.
“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.”
The charity has also suggested introducing beavers into the Cairngorms National Park, saying the animals would benefit from the environment and cause minimal conflict with landowners.
Mid Scotland and Fife Green MSP Mark Ruskell said the figures were shocking.
“The fact that a fifth of Scotland’s beaver population has been killed as part of an accreditation, management and licensing framework is nothing less than a scandal,” he said.
“It’s hard to see how this is compliant with either the spirit or the letter of the European laws which are supposed to protect beavers.
“SNH’s conservation role needs to be focused on ensuring vested economic interests are not put above Scotland’s protected wildlife.”