Lee Sang-min said he was stepping down from his post "as a sign of deep responsibility for not serving the public and the president well," according to the JoongAng Ilbo newspaper.
President Yoon Seok Yol has accepted his resignation, the paper added.
Lee and Yoon are among those being investigated for alleged sedition following the declaration of martial law on December 3.
Yun, who narrowly survived an impeachment motion in parliament on December 7, was forced to lift martial law after lawmakers voted against his decree.
On 8 December, police arrested Kim Yong-hyeon, who was defence minister at the time martial law was imposed.
Kim had already been banned from travelling. | BGNES
