An expert report has called for hundreds of thousands of deer to be culled in Scotland to deal with an unsustainable surge in numbers.

The report estimates that up to 1 million wild deer could be roaming Scotland, nearly double some previous estimates, causing significant damage to the landscape and hampering calls to increase tree cover to tackle the climate crisis.

Roughly half of those are red deer, a species closely associated with the Scottish Highlands, often roaming in vast herds. Conservationists argue they prevent woodland and shrubs from naturally regenerating.

Among nearly 100 recommendations, the report urges Scottish ministers to crack down on uncooperative Highland estates that refuse to control numbers in order to protect their lucrative deer-hunting market, by using legal powers to enforce culls.

The deer working group report says Scottish Natural Heritage (SNH), the government agency that polices deer legislation, should use its enforcement powers, including emergency measures, to cull out-of-control deer herds.

It says the maximum average density of deer across Scotland should be capped at 10 per square kilometre, and densities often need to be much lower in some sensitive or over-grazed areas.

Some deer estates in areas such as Glen Artney and Strathtay Perthshire have red deer densities above 20 per square kilometre, while numerous parts of Inverness-shire, the Cairngorms, Deeside and Angus have between 15 and 18 per square kilometre.

The report endorses SNH’s identification of the need for significant changes in deer management as an important issue in climate crisis mitigation measures, and recommends that it is addressed as a priority.

Alex Hogg, the chair of the Scottish Gamekeepers Association, said the report was another ‘hammer blow’ to the shooting industry. Photograph: Jeff J Mitchell/Getty Images

Among a series of proposals that have particularly alarmed landowners and the shooting industry, it has called for the closed season for stags to end, allowing male deer to be shot year-round, and for a much more restricted closed season for hinds, limited to the breeding season.

The Scottish Gamekeepers Association (SGA) said the industry was already worried by “damaging” demands recently for much tighter regulation of grouse shooting in Scotland.

Alex Hogg, the SGA’s chairman, called for urgent talks with ministers. “This sector is getting tired of being kicked from pillar to post and this report, which basically signals a free-for-all on an iconic Scottish species, is a further hammer blow,” he said.

Richard Cooke, the chair of the Association of Deer Management Groups, the umbrella body for the voluntary groups that oversee voluntary deer culling efforts, said the report offered some welcome ideas for tidying up the law but was in reality seeking heavy cuts in deer numbers.

That “would have a devastating effect on an important rural industry in the remoter parts of Scotland and there is a real danger if we continue to demonise deer that we overlook the multiple other impacts on our environment”, he said.

Roseanna Cunningham, the Scottish environment secretary, said she needed to reflect and would consult widely before deciding what action the government should take. It was an “important and complex issue”, she said.

The report says ministers should let stalkers use night sights, to allow for shooting in darker conditions. It proposes banning the use of lead bullets and urges far greater controls on deer herds near major roads, to cope with a rise in collisions with vehicles.

The working group, which was first chaired by Simon Pepper, a widely respected conservationist who died before the report was completed, stopped short of putting a number on how many deer needed to be culled in total each year.

It said there were significant challenges in pinpointing an accurate figure for Scotland’s overall deer population. One report in 2004 said there were 543,500; another in 2010 estimated between 574,000 and 777,000; and SNH said in 2013 there were between 593,000 and 783,000.

Official figures collated by SNH significantly underestimate the number of red, roe, fallow and sika deer living wild, the working group concluded, because they relied heavily on national cull data, which was incomplete.

Roseanna Cunningham, the Scottish environment minister, says deer culling is an “important and complex issue”. Photograph: Murdo Macleod/The Guardian

The official data showed that between 100,000 and 130,000 deer were shot each year in Scotland. SNH admitted to the group its national cull data only covered about 90% of red deer shot, 75% of the sika and fallow culls and only 40% of the roe deer cull.

The working group said that suggested another 70,000 deer were being culled each year without being centrally recorded, suggesting an average annual cull of 180,000. At the same time, roughly 20,000 more deer were dying naturally or being killed in traffic collisions.

“This level of annual mortality could be considered to suggest that the overall population of wild deer in Scotland is higher than the previous estimates that SNH cites and could potentially be approaching a million,” the report says.

Urging SNH to produce far more accurate deer number data and maps, the group said that although red deer numbers in the Highlands appeared to be static, they were spreading elsewhere in Scotland because of global heating and increased habitat availability.

While the report’s authors were cautious about fixing a higher culling figure for red deer, they said the annual roe deer cull should double to about 90,000 a year. Conservationists believe Scotland’s red deer population, estimated at between 350,000 and 400,000, could be cut to about 133,000 and still allow 12,000 stags a year to be shot.

Duncan Orr-Ewing, the chair of the deer task force at Scottish Countryside Link, an umbrella body for conservation and environment groups, said the recommendations were welcome.

Excessive deer numbers were damaging nature conservation goals, he said. “These outcomes include woodland expansion; peatland protection and restoration as vital carbon stores; enhancing the condition of protected nature conservation sites; and reducing vehicle collisions and the spread of Lyme disease.”