Four dairy cows were confirmed to have contracted the disease after authorities examined them upon receiving a report from the farm's owner, Yonhap news agency reported, citing the ministry.
South Korea's first case of this year was confirmed in cattle on a livestock farm in Anseong, some 65 km south of Seoul, on August 12.
To prevent further infections, the government has cordoned off the affected farm and implemented quarantine measures, the ministry said.
The infected cows will also be culled in accordance with relevant guidelines.
LSD is a highly infectious disease that causes skin lesions, fever and loss of appetite, often leading to a fall in milk production and even death. It affects cattle and buffalo via mosquitoes and other blood-feeding insects.