The website of the presidential office was one of several official and media sites hit by an apparently co-ordinated attack on Tuesday morning, reports said.
The identity of the hackers was not known, a government statement said.
The incident came on the anniversary of the start of the 1950-53 Korean War, which divided the Korean peninsula.
“The government can confirm a cyber attack by unidentified hackers that shut down several sites including the Blue House,” the Science Ministry said in a statement, referring to the presidential office.
The website for the office for Government Policy Co-ordination and some media servers were also said to be affected by the attack.
Messages praising North Korean leader Kim Jong-un and claiming that hacking collective Anonymous was responsible were left on the hacked websites.
However, Anonymous denied any involvement in the South Korean cyber-attacks on its official Twitter account, AFP news agency reported.
Instead, the “hacktivist” group was said to have planned attacks against North Korean websites.
A number of North Korean websites went offline on Tuesday morning and appeared to have been targeted by hackers on Tuesday, South Korea’s Yonhap news agency reported, citing unnamed sources.
These included the websites of North Korea’s Korean Central News Agency, newspaper Rodong Sinmun, and portal Naenara.
Anonymous has previously claimed to have hacked and vandalized social networking profiles linked to North Korea as part of its Operation Free Korea.
South Korea has raised its cyber-alert level, and asked citizens to review their internet security.
South Korean investigators say North Korea has frequently carried out cyber attacks in the South.
On March 20, cyber attacks on six South Korean banks and broadcasters affected 32,000 computers and disrupted banking services.
South Korea has blamed that incident – which came at a time of heightened tensions between the two Koreas following Pyongyang’s nuclear test on February 12 – on North Korea.
North Korea has also been blamed for previous cyber attacks in 2009 and 2011.
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