The hacking originated from 16 servers based in the North's capital Pyongyang, police said, adding the North had stolen more than 42,000 internal records.
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The North gained access to the internal systems of the firms and agencies at some point after hacking in 2014 into computer management software developed by a Seoul IT firm, according to the police.
The breach was discovered earlier this year.
The hackers also planted 33 types of malicious code into the computers in an apparent bid to use them as "zombie" machines to launch future cyberattacks on other organisations in the South, it said.
The companies that were hacked include South Korea's flagship air carrier Korean Air and SK Networks, a sister company of South Korea's top wireless operator, SK Telecom, Yonhap news agency said.
"We worked with the organisations that were targeted to recover the lost records and fortify their computer security to prevent further infiltration," the police said in a statement.
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The records include designs of military aircraft and Internet facilities at South Korean army barracks, according to the Yonhap.
Police added that some of the 16 servers in Pyongyang had the same IP addresses as those that had staged a crippling cyberattack on Seoul's banks and TV broadcasters in 2013.
Seoul has in recent years blamed the North's hackers for a series of cyberattacks on military institutions, banks, state agencies, TV broadcasters, media websites and a nuclear power plant.
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The attack in March 2013 left the websites and tens of thousands of computers at several TV stations and banks paralysed for hours.
Pyongyang has angrily denied involvement in the attacks and accused Seoul of spreading fabrications aimed at slandering its leader.
The North operates an army of more than 1,000 hackers who stage hacking or cyberattacks targeting Seoul's major institutions or key officials, according to the South's spy agency.
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