The carcass was in a drainage ditch in Franklin County, CNN reported. The agents from the Department of Wildlife and Fisheries who found it were not sure if the bird was killed somewhere else.
"To see any protected animal decapitated in a ditch is disheartening enough, let alone the animal that represents our symbol of freedom," Capt. Alan Bankston of the wildlife department said in a press release.
Bankston said those who provide information that leads to an arrest could receive a reward of as much as $2,000.
Adam Einck, a spokesman for the department, said the bird appeared to have been dead about two days when it was found. He said a necropsy had not been performed as of Tuesday.
Bald eagles are protected by the Bald and Golden Eagle Protection Act.