Prosecutor General Han Sang-dae offered his resignation Friday during a news conference, saying he would step aside so a successor could oversee reforms in the office, Yonhap News Agency reported.
"As the prosecutor general, I offer my apology to the people for a huge shock and disappointment," Han said.
South Korean President Lee Myung-bak has accepted Han's resignation, saying the prosecution "needs a self-reflection."
A group of top prosecutors in Seoul Thursday demanded Han's resignation, asking him to take responsibility for several scandals, including bribery and sexual misconduct involving sitting prosecutors.
Deputy Prosecutor Chae Dong-wook will handle Han's duties until a new lead prosecutor is named.
Han resigned after he canceled plans to announce a package of reform measures for the office and how it operates, Yonhap said.
Han's three-year term was to end in 2014. He is the 11th chief prosecutor to resign before completing the three-year tenure. His predecessor, Kim Joon-gyu, stepped down in July 2011 to protest parliamentary approval of a bill limiting the office's investigatory power.
Justice Minister Kwon Jae-jin also apologized Friday for the incidents that eventually led to Han's resignation.
"As the justice minister who commands the prosecution, I feel deeply responsible and offer my apology," Kwon said in a statement.