The year-old white-tailed sea eagle had been brought over from Norway in 2008 as part of a reintroduction programme.
It was found decomposed on the Glenogil Estate, a popular grouse shooting estate in Angus. Tests confirmed the eagle, known as Bird 89, had been poisoned with the banned pesticide carbofuran.
The estate is owned by John Dodd, who was co-founder of Artemis Investment Management. He sold his stake for 50 million in autumn 2008.
Two years ago another sea eagle, known as White G, was found poisoned on the boundary of the Glenogil estate. It had also been poisoned with carbofuran.
And in September 2008 Mr Dodd had a record 107,000 of his farm subsidy docked by the Scottish Government, after illegal pesticides were discovered on his land in 2006.
Mr Dodd is appealing against the decision. He has always maintained the innocence of himself and his staff.
Tayside Police said Bird 89 was "likely to have ingested bait laced with banned agricultural pesticides that were deliberately set out".
Killing or attempting to kill a bird of prey is punishable by a six-month jail term and/or a 5,000 fine under the Wildlife and Countryside Act.
The dead bird was discovered on 6 August, but Tayside Police have only now made the find public after The Scotsman questioned them about the incident.
Detective Inspector Ally Waghorn said: "It is an absolute disgrace that the use of pesticides to kill what are seen by some as pest species continues in Scotland.
"There is also a real risk to any hillwalker who might encounter and handle the poisoned bait."
Bird 89 was one of 15 sea eagles donated to Scotland by Norway in June 2008 as part of a five-year, 358,000 reintroduction programme, half-paid for from the public purse.
Duncan Orr Ewing, head of species and land management at RSPB Scotland, said it was an "utterly despicable crime" and pointed out that "once again it has been found in an area where sporting estates dominate the landscape".
He said the "litany of incidents" in "certain parts of the Angus Glens" should "justify the deployment of all possible resources to identify those responsible and then consider the full range of sanctions to tackle the perpetrators".
Environment minister Roseanna Cunningham condemned the "appalling crime against a magnificent bird of prey. It is a cruel irony that the sea eagle, reintroduced following extinction, is still being persecuted".
Mr Dodd was not available for comment.
Trail of illegal poisonings that leads to shooting estate
PREVIOUS incidents of suspected wildlife crime on or close to Glenogil Estate include:
May 2006: Suspected rabbit poisoned bait found – tests by Science and Advice for Scottish Agriculture lab confirmed it had been laced with outlawed pesticide carbofuran.
June 2006: Bait found laced with carbofuran, also found on equipment and vehicles. Estate owner John Dodd subsequently had 107,000 withdrawn from his single farm payment subsidy by the Scottish Government. He is appealing against this.
November 2007: Tayside Police informed a white-tailed eagle had been shot by a Glenogil estate employee. No carcase was found, but the bird, fitted with a radio transmitter, is still missing.
May 2008: A white-tailed eagle known as White G was found dead by a neighbouring landowner. It had been poisoned with carbofuran and other pesticides.
Three days later, Tayside Police and RSPB staff found the carcase of a buzzard lying next to the Glenogil Estate boundary fence. It had been poisoned. Carcase of a hare was found to have been laced with same chemicals that killed eagle.
October 2008: A meat bait is found on a fence post within Glenogil Estate, laced with an illegal chemical mix.
August 2009: Dead white-tailed eagle found on estate, poisoned with carbofuran.
March 2009: Two dead buzzards found on the estate. Both birds had been poisoned.
SCOTLAND'S first wildlife crime education programme for schoolchildren was launched in the Highlands yesterday. The project has been created by Northern Constabulary and the Royal Zoological Society of Scotland, which owns the Highland Wildlife Park at Kincraig. Each school in the Highlands will be able to send senior pupils to be given tuition by experts.