Marty and Teddy Fleming are both charged with second-degree animal cruelty.
On March 16, deputies with the Letcher County Sheriff's Department said they found more than 10 dogs, living in bad conditions. They also said they found evidence to support a puppy mill.
Some of the dogs were in small cages and standing in their own feces.
On Thursday, investigators searched the home where the animals were kept. They said many of the dogs they saw during their initial search had been removed from the property.
"He's obviously moved them for some reason," said Sergeant Alisha Congleton, with the Letcher County Sheriff's Department. "Like he felt like he was doing something wrong. Every animal that was up here the other day has been moved or tampered with."
Deputies said Marty Fleming was nowhere to be found when they did the search. However, deputies spoke with his father, Teddy Fleming, at the scene.