The spy, identified as Jung Gyong Hak, was attempting to enter South Korea with a forged passport from a Southeast Asian country, the National Intelligence Service said.
Jung had previously stayed in South Korea with a Thai passport in 1996-1997, and was caught by the intelligence service while trying to re-enter using a fake passport from the Philippines in late July.
He was sent to Seoul Prosecution last week, which was expected to indict the suspected North Korean spy, officials said.
Jung is believed to be a member of an espionage arm of the North's ruling Workers' Party, they said.
The suspect is the first alleged North Korean spy to be arrested since 2003 while trying to enter the country.
The intelligence agency has exposed eight North and South Koreans for spying for the North since President Roh Moo-hyun took office in early 2003.
The spy case comes at a time when military tensions are rising across the inter-Korean border over North Korea's programs to develop ballistic missiles and nuclear weapons. North and South Korea are still technically in a state of war, as the 1950-53 Korean War ended without a peace treaty.
Notable deaths of 2014 [PHOTOS]