Among several official and media sites hit by an apparently coordinated attack was the website of the country's presidential office, officials said.
"The government can confirm a cyberattack by unidentified hackers that shut down several sites including the Blue House," Korea's Science Ministry said in a statement, referring to the presidential office.
The incident came on the anniversary of the outbreak of the 1950-53 Korean War, which divided the Korean Peninsula into North and South.
Messages praising North Korean leader Kim Jong-un and claiming that hacking collective Anonymous was responsible were left on the hacked websites, the BBC reported.
Anonymous has denied any involvement in the hacking.
South Korean investigators allege North Korea has frequently carried out cyberattacks on the South, including an attack on websites of banks and broadcasters in March.