Wild beavers have colonised lochs and rivers across the southern Highlands of Scotland after a sharp surge in their numbers.

A survey by NatureScot, the government conservation agency, estimates 1,000 beavers now live in the wild, reaching rivers north of Dundee in the east, westwards to Crianlarich, north of Loch Lomond, and south to Stirling on the river Forth.

The largest of its kind so far in the UK, the survey confirmed beavers had established 251 territories, more than double (120%) those found three years ago. One northerly population in Glen Isla, Angus, is close to the southern border of the Cairngorms national park.

Using canoes and field surveys, researchers found 13,204 confirmed signs of activity, including burrows, dams, lodges, scent mounds, canal digging and tree feeding. There were signs of beavers near Drymen, next to Loch Lomond, but no evidence they had settled there.

NatureScot said those findings were a conservation success but the agency came under heavy criticism after disclosing 115 beavers had been killed last year under licence, to protect farms, woodland and infrastructure. Another 31 were trapped and relocated to official reintroduction sites in England and Wales.

Trees for Life, a rewilding charity, accused the agency of suppressing this data when the charity launched legal action over its beaver culling policy last year. Trees for Life is waiting for a judge to rule on whether NatureScot’s policy on lethal control is lawful, after a two-day judicial review hearing in June.

Alan McDonnell, the charity’s conservation director, said: “NatureScot has sat on this grim tally since December, refusing to confirm it until today’s bid to hide the figures behind a welcome turn of events for the overall beaver population. This is such a waste of life and opportunity when nature is in crisis.”

Environmentalists believe NatureScot and the Scottish government have failed to prioritise non-lethal control methods under intense pressure from farmers and landowners – a dispute which has implications for future rewilding and species reintroduction policies.

The National Farmers Union Scotland and NatureScot have said the current approach is proportionate, and culling was a last resort. The agency said it helped with 68 projects to protect farms and riverbanks, including fencing off trees, dismantling beaver dams or putting “flow devices” into them.

Robbie Kernahan, NatureScot’s head of sustainable growth, said: “Beavers are nature’s supreme water engineers, but we know they may cause severe problems in some areas, particularly for crops on prime agricultural land and for important infrastructure like road drains or railway lines.”