The red kite was discovered by a member of the public at Daintry Wood near Toddington.
An X-ray image showed it had 10 pieces of lead shot lodged in its body.
The RSPB said: "This was clearly no accident and it is especially sad considering the lengths that have been taken to reintroduce these splendid birds to England."
RSPB inspector Jenny Shelton said: "The bird will most likely have been shot at close range to incur this level of damage.
"Red kites feed mainly on carrion, so there is no logical reason for these birds to be targeted".
Bedfordshire Police has appealed for information about the shooting.
Insp Mark Farrant said: "This is a particularly worrying incident against a bird that is fully protected under the Wildlife and Countryside Act.
"I would ask anyone with information relating to this or similar incidents to call Bedfordshire Police."
According to the RSPB, the shooting of birds of prey is a widespread problem in the UK.
The organisation's latest Bird Crime report said there were 196 reports of shooting, trapping and destruction of birds of prey in 2015, including red kites.
The species is protected under schedule 1 of the Wildlife and Countryside Act 1981 and the punishment for killing one is up to six months in jail and/or a fine of up to Â£5,000.
Red kites became extinct in England in 1871, with only a handful of pairs left in remote parts of central Wales.
The RSPB helped reintroduce them in 1989 and there are now about 1,000 red kites in England.
A protected bird of prey has been found dead in Bedfordshire and had likely been shot "at close range".