The discovery was made Tuesday as the Monterey County SPCA and Seaside police served search warrants at the two properties, Bay City News Service reported.
The company that manages the properties alerted the SPCA after finding dead kittens at the properties.
"It's very disturbing," SPCA humane investigation supervisor Capt. Judi Adams said, adding all the dead felines were very young, "newborn, a day or a week old."
SPCA workers also seized 51 live adult cats, all in poor health, on the properties, Adams said. No live kittens were found during the search.
Adams said SPCA workers also found the professionally cremated remains of 40 to 50 other felines, all of which had the names and dates of death.
Medical examiners did not yet know how the kittens died, Adams said. All of the living cats were brought to the SPCA.
The investigation is ongoing and no arrests have been made.