Operation Migration said the male was dead when the pair were found in November in Hopkins County, and the female was so badly injured she had to be put down. A necropsy found bullet fragments in one of the birds.
The killing was only announced this week.
The cranes were graduates of a program that uses light aircraft to teach young birds how to migrate, the group said.
The U.S. Fish and Wildlife Service and conservation groups are putting together a reward package for information leading to an arrest.
John Brunjes, a biologist with the Kentucky Department of Fish and Wildlife Services, told the (Louisville) Courier-Journal the birds were almost certainly not shot by hunters, who would have been using shotguns.
"It's jerks, riding around with a gun, shooting at anything that moves," he said.
The whooping crane is highly endangered. In 2011, there were believed to be 437 cranes in the wild and 165 in captivity.
Until recently, all remaining cranes nested in a small area in Alberta, Canada, but were recently reintroduced in Wisconsin. They winter on the Texas coast.