The cyber attacks took place last month, on the anniversary of the beginning of the 1950-53 Korean War which left the peninsula divided between the rival countries.
North Korea has been suspected of masterminding previous cyber attacks on South Korea, including one in March that paralysed tens of thousands of computers and servers at major broadcasters and banks.
North Korea has repeatedly denied responsibility for such attacks saying it has also been a victim of hacking.
South Korean officials said they had detected North Korean involvement in the latest cyber assault that shut down several sites including those of the presidential office and the conservative ruling party.
"An IP address within North Korea's bandwidth was found," Chun Kilsoo, an official at the state-run Korea Internet and Security Agency, told a briefing, referring to a computer's internet protocol address.
The malicious computer codes and technique of the attack were similar to those detected in previous hacking attacks traced to the North, officials added.
The accusation comes as the two Koreas wrangle over the reopening of a joint factory park just inside North Korea that North Korea closed during a period of tension that began when it conducted its third nuclear test in February.
South Korea has not confirmed findings by U.S. online security company McAfee that a group of hackers was behind a string of cyber attacks on South Korea dating back to 2009 aimed at spying on its military.
South Korea's defence minister said at a recent conference that North Korea had about 3,000 highly trained cyber warfare personnel, according to media reports.
In March, the North suggested the United States was behind cyber attacks on its internet servers after reports of disruptions to its main news services.
A hacker collective known as Anonymous said it had attacked North Korean websites on the anniversary of the Korean War.
The group denied through Twitter posts any involvement in attacks on South Korea.
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