The farms in the southeastern city of Andong have been quarantined and a total of 9,000 pigs on the two properties will be slaughtered, the agriculture ministry said.
All cloven-hoofed animals within a radius of three kilometres (two miles) of the farms would also be culled, the ministry said. Officials are investigating the cause of the outbreak.
Previous outbreaks in January and April cost more than 250 billion won (216 million dollars) and left nearly 50,000 animals slaughtered.
Foot-and-mouth disease affects cloven-hoofed animals such as cattle, pigs, deer, goats and sheep.
South Korea ordered a halt to pork and beef exports in January when an outbreak was confirmed at Pocheon northeast of Seoul.