The dead cats were found in a freezer and refrigerator in the downtown apartment last month, while another 49 cats were found alive.
Windsor-Essex County Humane Society director Melanie Coulter says it appears the cats died from health issues and not any kind of violence.
But she says authorities believe the animals did not receive adequate veterinary care.
Jerry Miernecki is charged with failing to comply with an order and permitting cats to be in distress under the Ontario Society for the Prevention of Cruelty to Animals Act.
He's expected to make a court appearance March 4.
Coulter says investigators don't believe anything malicious was intended when the dead cats were placed in the freezer but that it may have been a way to keep them until they could be buried.
"There were medical issues ... we believe they didn't receive adequate vet care," Coulter said. "But it wasn't an incident where they were the victim of violence, we believe."
Some of the surviving cats are available for adoption while others are still being treated.