The new figure, disclosed in a ministry white paper, comes after the United States, South Korea's key ally, imposed new sanctions on North Korea for a cyberattack on Sony Pictures Entertainment. Pyongyang has denied involvement in the attack.
For years, North Korea has been pouring resources into a sophisticated cyber-warfare cell called Bureau 121, run by the military's spy agency and staffed by some of the most talented computer experts in the country.
Its long-term target may be telecoms and energy grids in rival nations, defectors from the isolated state said.
"North Korea is currently running its 6,000 (-member) workforce for cyber warfare and performing cyber attacks for physical and psychological paralysis inside South Korea such as causing troubles for military operations and national infrastructures," the South Korean Defense Ministry said.
North Korea has denied involvement in the recent hack into Sony Pictures, which distributed a comedy film featuring an assassination plot against its leader Kim Jong Un and slammed the fresh U.S. sanctions, calling them hostile and repressive policies by Washington.
The reclusive country is also suspected to have carried out a series of other cyber attacks against South Korea, which it is technically at war with.
In 2013, South Korea blamed the North for crippling cyber-attacks that froze the computer systems of its banks and broadcasters for days.
The two Koreas have remained technically at war for more than six decades as the Korean War ended in an armistice, not a peace treaty.