They said it was the first report of a cat having had the virus since a case in Thailand in 1996, but that there was little risk to humans as there has never been a known transmission of the virus from a cat to other mammals.
"It is quite rare for a cat to be infected by the avian flu virus," said Cho Hyun-Ho, a deputy director of the National Veterinary Research and Quarantine Service.
Cats and dogs are usually not susceptible to the virus, so quarantine officials only normally check animals that have regular contact with birds.
The cat was found dead in April in Gimje, about 250 kilometres (150 miles) south of Seoul.
"It probably had eaten a sick bird or came in very close contact with chickens or ducks," an unidentified quarantine inspector told Yonhap news agency.
Gimje was one of the first regions hit by South Korea's latest bird flu outbreak, which began in early April and swept through most of the country for nearly two months.
Nearly 8.5 million birds have been put down since the outbreak and the overall cost has been estimated at 264 billion won (262 million dollars).
South Korea has been hit by bird flu outbreaks three times. But no South Korean is known to have contracted the disease, even though the H5N1 strain has killed more than 240 people worldwide since late 2003.
Scientists fear the virus will eventually mutate into a form that is much more easily transmissible between humans, triggering a global pandemic.