The eight- year-old bird was rescued and x-rayed by local falconry specialist vet, Mark Naguib, after she was discovered in the grounds of Selby Abbey on May 7.
Mr Naguib found a number of shotgun pellets throughout the bird's body.
The peregrine is ringed by the British Ornithology Trust so was able to be traced back to being released as a chick near Newark eight years ago.
She is now in the expert care of local wildlife rehabilitator, Jean Thorpe, who will give her the best possible chance of making a recovery.
North Yorkshire Police Constable Sarah Ward said: “Peregrine falcons are a protected schedule one species and it is shocking that anyone would target one in this cruel and callous way.
“Our county should be a haven for birds of prey and this type of cruelty will not be tolerated."
RSPB Investigations Officer, Jack Ashton-Booth added: “We are appalled at this deliberate and illegal attack on a protected peregrine falcon. The bird was riddled with shot, including one piece lodged in its head. Incredibly, it is still alive but it’s touch and go."
Anyone with information is urged to call police on 101, or alternatively call Crimestoppers anonymously on 0800 555 111.