Police said the birds were discovered in Oakley Wood, near Crowmarsh Gifford, Oxfordshire.
It is not clear how the dead kite was killed, but the two injured birds had been shot with a shotgun.
Red kites are protected under the Wildlife and Countryside Act 1981 and anyone found killing one can face jail.
The surviving birds are now being cared for by the Tiggywinkles charity.
PC Robert Searle, of Thames Valley Police, said: "Fortunately incidents of this nature are very rare in the Thames Valley and a thorough investigation is under way."
The Chilterns Conservation Board said the reintroduction of red kites on the Oxfordshire-Buckinghamshire border in 1989 was one of the UK's most successful conservation projects.
There are about 1,000 red kites in England.
A red kite, one of the UK's most highly protected birds of prey, has been found dead and two more left riddled with shotgun pellets.