The latest case was reported on a farm raising around 22,000 ducks in Changnyeong, 264 kilometres southeast of Seoul, according to the Ministry of Agriculture, Food and Rural Affairs, reports Yonhap news agency.
It marked South Korea's first highly pathogenic avian influenza case since February 8, when a case was reported at another duck farm in Asan, 90 km south of Seoul.
The agriculture ministry said it is currently taking preemptive measures, including controlling entry to the farm, as well as culling affected birds.
It has also issued a 24-hour standstill order for the area to prevent the spread of the disease.
Highly pathogenic avian influenza is very contagious among birds and can cause severe illness and even death, especially in domestic poultry.