It said migratory and resident wild birds would be monitored regularly and all chicken and duck farms would be inspected every other week for both the virulent and less contagious strains of avian influenza.
Some 23 monitoring teams will be established nationwide.
Quarantine authorities were caught by surprise when an outbreak began in early April and swept through most of the country.
In the past a heightened bird flu alert was in force from November to March, when migratory birds stay in the country and weather conditions may help spread the virus.
The government culled more than eight million birds and the cost of the outbreak was estimated at 264 billion won (259 million dollars).
No confirmed case has been reported since May 12. If no other case emerges, the agriculture ministry will declare South Korea free of the disease in August.
The ministry said the country's 2,384 duck farms would be watched especially closely because ducks have longer incubation periods and were found to be the main cause of the spread of bird flu.
"Because of this decision, the government will require even small duck farms to be registered so they can be checked," Lee Sang-Kil, head of the ministry's livestock policy bureau, was quoted by Yonhap news agency as saying.
Following outbreaks in major cities including Seoul and Busan, a new standard operating procedure would be formulated for urban areas.
The country has been hit by bird flu outbreaks three times. But no South Korean is known to have contracted the disease, even though the H5N1 strain found here has killed more than 240 people worldwide since late 2003.