Grouse moor owners in Scotland face heavy fines or prosecution for failing to protect birds of prey and other species under proposals to licence shooting estates.

An expert report for the Scottish government has recommended ministers introduce mandatory licensing of grouse moors within five years because of their associations with the systematic persecution of eagles and other protected birds.

The panel chaired by Prof Alan Werritty, a geographer, was set up by ministers after an expert report directly linked driven grouse moors to the disappearance of 30% of all golden eagles in parts of the Highlands.

Grouse moors managers are blamed by conservationists for the illegal killing and disappearance of thousands of birds of prey to protect grouse stocks. Gamekeepers have been prosecuted for using poisoned baits, traps, shooting and nest disturbance, while several estates have been banned from controlling birds because of suspected links to persecution.

The Werritty report said licensing would allow Scottish Natural Heritage, a government agency, to control the unnecessary culling of mountain hares, the over-zealous burning of heather causing environmental damage and the overuse of medicated grit, used to control infections in grouse stocks.

It is understood Nicola Sturgeon, the first minister, wants to introduce licensing much sooner than 2024, despite opposition from land owners and shooting estate managers, as do Roseanna Cunningham, the Scottish environment secretary, and Mike Russell, the Brexit secretary who pushed through tougher regulation of wildlife crime as environment minister.

Pressed by Scottish Green party and Scottish Labour MSPs to take urgent action at first minister’s questions, Sturgeon said earlier implementation “absolutely needs to be considered.” She said: “A clear part of that consideration [of the report] will be looking at whether to move to regulation in a much quicker timeframe.”

Prominent pro-shooting organisations, including the landowners’ body Scottish Land & Estates, the Scottish Countryside Alliance and the Scottish Gamekeepers Association, were furious.

Although the Werritty review rejected calls from animal rights groups to outlaw driven-grouse moors, they said: “The recommendations of the Werritty review will mean a seismic change for grouse moors across Scotland.

“This report has recommended a barrage of measures that will leave the grouse-shooting sector engulfed by legislation and red tape. On top of that, penalties for wildlife crime in Scotland are about to get much tougher.”

In a parallel development, conservation sources said grouse moors in England would soon be banned from burning heather, a process known as muirburn, on climate and environmental grounds – a step Scottish ministers are not expected to take.

Werritty said his committee would not agree to the immediate licensing of grouse moors because two members had objected to his decision to use his casting vote to make that recommendation.

It is understood that the two members are Mark Oddy, a former director of Buccleuch Estates, and Alexander Jameson, an estate management consultant. A source close to both men denied that both had threatened to resign and produce a minority report if he did so.

Werritty said to achieve unanimity, the committee agreed to give grouse moors until 2024 to prove that golden eagle, hen harrier and peregrine numbers in their vicinity were in favourable condition or face licensing.

He said: “Because the evidence base is so heavily contested, reaching a unanimous recommendation was fraught – personal opinions and values intervened. But we did agree that any decision on licensing is ultimately a political one in which wider societal views also need to be taken into account.”

He said SNH should be given the same legal powers as the Scottish Environment Protection Agency, which monitors pollution, to impose fixed or variable fines, or “in the event of serious, deliberate or persistent breaches of the law” move to criminal prosecution.

The pro-shooting groups said there were much tougher laws being implemented to limit illegal behaviour in their industry, including five-year jail terms for raptor persecution, the right under civil law for SNH to punish landowners if wildlife crime offences happen on their estates.

The Royal Society for the Protection of Birds and Revive, a coalition of anti-shooting groups, said Werritty should have been far braver.

Duncan Orr-Ewing, the head of species and land management for RSPB Scotland, said: “The illegal killing of Scotland’s birds of prey simply has to stop. [It] is now vital that the next steps by Scottish government are sufficient to bring closure to these appalling incidents, which blight Scotland’s international reputation.”