The Ministry of Agriculture, Food and Rural Affairs said the case reported at a farm in the southwestern county of Gochang, about 300 km from Seoul, was of the highly pathogenic H5N8 strain.
A cull of 21,000 birds at the farm has been completed and authorities are widening the cull to a 3km radius of the site but there are no indications of a wider spread of the outbreak, a ministry official said on Saturday.
The strain was previously identified in a 2010 case reported in China and is largely similar to the H5N1 type, South Korea's Yonhap news agency said.
Asia's fourth-largest economy has had four outbreaks of the virus in the past 10 years, the most recent in 2011, which led to the slaughter of more than 3 million poultry, but no human cases of the bird flu strain have been reported.
In Asia, around 150 people in China, Taiwan and Hong Kong have been infected by a new H7N9 strain of bird flu since it emerged in China last year, claiming at least 46 lives.
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