Officials removed the cats from a home in Wright, near Albany, on Wednesday night.
The Times Union of Albany reports the dead cats were packed in plastic bags in the freezer and the live cats were in crates stacked floor to ceiling.
Sheriff's deputies went to the home after a neighbor called to complain about the overpowering odor of cat urine and feces.
Charges are being weighed against the cats' owner.
The manager of the animal shelter that took in the cats said she previously tried to try to help the woman. But she said the woman had "a hoarder mentality."