"The culling could continue well into the night, though it remains unclear when it will end," Park Sung-soon, an official handling the issue at the Jeju Special Self-Governing Province, told Yonhap News Agency via telephone.
Quarantine officials have already killed 38,000 chickens and ducks across the country, including 10,400 on Jeju, since Friday when a suspected bird flu was reported at a chicken farm on the island.
The Ministry of Agriculture, Food and Rural Affairs said Monday that the outbreak -- the first in two months in South Korea -- was caused by a highly pathogenic strain of H5N8.
Highly pathogenic avian influenza refers to viruses that cause severe disease in birds and result in high death rates, according to the World Health Organization.
South Korea slaughtered more than 30 million poultry to contain the worst outbreak of bird flu that hit the country in November.
South Korea culled 14 million birds in 2014. (Yonhap)