RSPB Scotland said the discovery in Perthshire in May this year showed an attempt was made to cover up the illegal killing of the bird.
Details of the find near Dunkeld emerged following a months-long police forensic investigation.
A walker and his son found the lead package on a bank of the River Braan.
RSPB Scotland said the eagle’s tag stopped transmitting on a grouse moor in Perthshire in 2016. A search involving police did not find the bird.
The tag, confirmed as the eagle’s from its serial number, was found a few miles from the last known location of the bird.
RSPB Scotland said the incident was a further example of the persecution of birds of prey on land managed for grouse shooting.
The Scottish Gamekeepers Association (SGA) and landowners organisation Scottish Land and Estates said the disappearance of the bird and the discovery of the tag should be investigated by police.
But they said grouse moors had often been unfairly blamed for the disappearance of birds of prey.
Ian Thomson, RSPB Scotland’s head of investigations, said the disappearance of any satellite-tagged raptors disappearance over a grouse moor should be regarded as suspicious.
He said: “This young eagle was killed illegally. The tag was clearly removed from the bird, its antenna was cut off, and the tag was then wrapped in a piece of lead sheeting, presumably because the perpetrator thought this would stop it transmitting.
“The package was then cast into the river, never to be seen again. Or so they thought.”
Duncan Orr-Ewing, RSPB Scotland’s head of species and land management, said the incident further highlighted the need for tighter rules on the management of shooting estates.
The SGA said the disappearance of satellite-tagged birds had been “heavily weaponised” by political campaigners.
A spokesman said: “They elicit high levels of publicity and a person finding one on their land would not want it around, given the scrutiny they would come under.
“We will await to see what the police can uncover from the evidence. We hope they find the truth of what has happened, for everyone’s sake.”
Mark Tennant, chairman of Scottish Land and Estates, said his organisation would “fully support a thorough police investigation and any perpetrator being brought to justice”.
He added: “However, what must be questioned is the blatant use of alleged incidents in pursuit of a long held political objective of licensing grouse shooting.
“It is more than four years since this bird disappeared and four months since the satellite tag is claimed to have been discovered. Collaboration and cooperation with estates and other partners in the local area over this period should have been the basis for finding out what happened to the bird.”
Tayside and Central Scotland Moorland Group, said it was too easy to blame grouse moors, adding: “Hopefully the police can get to the bottom of it and people can be removed from unfair suspicion.”