The H5N6 virus was first confirmed on November 18 at a farm in central South Korea and it has since spread to farms around the country, with the total number of cases now standing at 46.
Authorities have stepped up quarantine measures, culling birds and restricting animal movements which are feared to spread the virus.
"We've culled some two million birds and we will slaughter another one million", an agricultural ministry spokesman told AFP.
However, between 2014 and April 2016, H5N6 killed six people in China, according to the South's Center for Disease Control and Prevention.
The World Health Organization warned earlier this year that the strain "has caused severe infection in humans" but added "until now human infections with the virus seem to be sporadic with no ongoing human to human transmission".