Gamekeepers have attacked the steep increase in the "immoral" culling of deer at night by stalkers who are paid a bounty for every deer they shoot.

Professional gamekeepers claim that deer are being inhumanely culled across Scotland, and are often left wounded or orphaned because freelance stalkers rely on being paid a bounty of up to £145 a head, rather than on a regular wage, and shoot at night without proper control.

Figures released to the Guardian by Scottish Natural Heritage, the government's conservation agency, show the number of deer shot at night has increased by nearly 50% in the last three years, while the overall number shot has fallen.

In 2008/9, 6,710 deer were shot at night, jumping to 9,933 last year. However, in the same period, the overall number of deer culled across Scotland fell from 98,893 down to 95,424. Night-time licences were also up, from 179 in 2008/9 to 226 last year.

Deer are often nocturnal and recent harsh winters have pushed tens of thousands off the hills into lower altitudes to find food and protection, increasing conflict with foresters and farmers.

Night-time shooting is known in the trade as "lamping", where marksmen take powerful all-terrain or 4x4 vehicles into forests, woodland and glens, using powerful spotlights to illuminate and confuse feeding deer before shooting them. Contractors earn between £64 and £145 a carcass, depending on the terrain.

Professional stalkers in the Highlands are so incensed by the increase of lamping that they have taken the unusual step of alerting Animal Aid, one of the country sports industry's greatest critics.

Andrew Tyler, Animal Aid's director, said: "That they are so desperate about the bounty culling of so many deer at night that they should come to an animal rights organisation really is an indicator that things are seriously wrong."

Full-time stalkers said night-shooting was intended as a last resort when other methods had failed. It is often more risky, because paying contractors by the head greatly increases the pressure on them to shoot at greater distances or shoot any animal in range.

They told the Guardian this meant there was an increased risk that females with young calves would be shot, leaving vulnerable calves orphaned. Contractors were more likely to wound deer when shooting at greater distances at night.

In some cases, culling would be far more intense and indiscriminate because freelance contractors wanted to earn as much as possible. It also means that mature stags of great value to commercial deerstalking estates were being shot hastily.

One full-time professional stalker on a Highland estate with 20 years experience, who asked not to be named, said he believed bounty and night shooting were being used because it was cheaper and faster than traditional stalking.

Deeply suspicious about the accuracy of the official night-time culling figures, the stalker said he believed the true number shot at night could be two or three times higher. "The whole contracting system is morally wrong; it's morally wrong to hire a man to control deer on a bounty basis. It promotes malpractice," he said.

"There's no way we can deny the deer population has to be controlled by a sensible and measured cull. But at the moment it isn't a measured cull. Whatever these guys see, they're shooting."

The Forestry Commission, which has been the focus of many complaints, robustly defended its use of night-culling and its contractors. Its night-shooting figures had fallen since 2008. There had been "totally unsubstantiated" allegations about its procedures.

"Claims made that we are increasing our night-time shooting are false and in fact the opposite is the case as over the years this has dropped significantly," a spokesman said.

"We've heard other false allegations over the professionalism of the contractors we use, however our standards are the highest possible. In reality, one of the commonest complaints from would-be contractors is that our conditions are so tough to meet."

Scottish Natural Heritage said a "responsible, rigorous" assessment system was used before night shooting licences were issued, including evidence that deer were really creating damage to woodland, crops or reforestry schemes.

Robbie Kernahan, the agency's wildlife operations manager, admitted there was no clear reason why night-culling had increased so much; it could be a combination of severe weather driving deer off the hills or an increase in the number of smaller woodland owners and farmers hiring contract stalkers.

He said night shooting was not always a last resort. In many cases, the measure was needed because that was when deer were active: about 20% of night-culling licenses were going to farmers.

"People do hold quite strong, traditional views as to how deer should be managed," he said.

Kernahan said no one had formally complained to Scottish Natural Heritage about malpractice or abuses of night-culling licences. "None of these concerns have come to me formally, saying 'we believe these authorisations are being misused'," he said. "If they did, we would be duty-bound to investigate. If people believe these are being abused, they need to let us know."