He branded the shooting "cruel" as he appealed for anyone with information about what happened to come forward.
Mr Flynn said: "This eagle has been caused tremendous pain and suffering. It became grounded after being shot, which caused the feathers on its tail and wings to break and meant it was unable to search for food.
"If the eagle hadn't been found on Saturday, it is very likely it would have starved to death."
He went on: "Golden eagles are extremely rare and it is very concerning that someone would deliberately try to injure or kill such a magnificent creature.
"As well as being cruel, injuring a wild bird is also a criminal offence under the Wildlife & Countryside Act 1981 and we are very keen to speak to anyone who has information about this incident."