Kim Ki-Jong, 55, also faces a separate charge of violence against a foreign envoy after slashing Mark Lippert with a paring knife in an assault that left the US envoy needing 80 stitches to a deep gash on his face, the Yonhap news agency said.
A formal warrant for his arrest was issued and he was taken into custody in Seoul, according to Yonhap.
The profile painted of Kim is that of a lone assailant with strong nationalist views who saw the United States as one of the main obstacles to the reunification of the divided Korean peninsula.
Any red flags such activities may have raised were only underlined by North Korea's reaction to the attack, which the official KCNA news agency described as "just punishment" and a valid "expression of resistance" to ongoing US-South Korea joint military exercises.
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Lippert's case is being handled by a special investigation team comprised of more than 100 prosecutors and police officers, and led by the anti-terrorism bureau of the Seoul Central District Prosecutors' Office.
"We are trying to find out whether he has violated the national security law," Yoon said.
Enacted in 1948 to protect the fledgling South Korean state from infiltration by the communist North, the law prohibits the spoken or written promotion of North Korean ideology, deeming any such activity to be "anti-state" and subject to up to seven years imprisonment.
Kim's home and office in western Seoul were searched today, with documents and computer hard drives removed for further examination, police said.
"No, nothing like that," he replied, saying the idea was "outrageous."
Yoon later said police had found "treasonous" books at Kim's home, and were particularly interested in items "suspected of being pro-North Korea in nature," without providing further details.