The agriculture ministry said the alert was lifted to the second highest level because the virulent strain of avian influenza has spread to four provinces since the first outbreak was confirmed on December 31.
There have been 16 confirmed cases in birds so far this winter.
"In light of the rapid spread of the disease there is a need to take more stringent measures," a ministry official told Yonhap news agency.
Under the new alert level all birds within a three-kilometre (two-mile) radius of an outbreak will be culled as a precautionary measure, up from 500 metres previously.
Quarantine authorities will press poultry farmers to carry out daily decontamination measures and limit contact with wild birds.
The ministry said six new bird flu cases have been reported in South Jeolla province in the southwest. It said all 134,900 ducks on affected farms have been ordered culled, along with other birds in the immediate vicinity.
South Korea has been hit by avian influenza three times before, with the last outbreak in April 2008.
The renewed bird flu scare came as farmers and health authorities struggle to curtail the country`s worst-ever outbreak of foot-and-mouth disease.
Authorities have ordered the culling of more than 1.4 million livestock since late November. (*)
Editor: Kunto Wibisono
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