Prosecutor General Han Sang-dae said in a news conference that he will step down leaving all reform tasks to his successor.
"As the prosecutor general, I offer my apology to the people for a huge shock and disappointment," Han said.
President Lee Myung-bak immediately accepted Han's resignation, saying that "the prosecution needs a self-reflection," according to the presidential office Cheong Wa Dae.
Until a new chief prosecutor is named, Chae Dong-wook, the deputy prosecutor general, will act in Han's place, according to the prosecution. Han's three-year term was to end in 2014.
Han became the 11th chief prosecutor to resign before completing the three-year tenure. His predecessor, Kim Joon-gyu, also stepped down from his post in July of last year, in protest over the parliamentary approval of a bill limiting the prosecution's investigatory power.
Han's resignation offer came after he canceled his earlier plan to announce a package of prosecution reform measures yielding to pressure from defiant prosecutors.
On Thursday, a group of ranking prosecutors in Seoul demanded Han's resignation, asking the top prosecutor to accept responsibility for successive scandals, including bribery and sex scandals involving incumbent prosecutors.
Earlier this month, a senior prosecutor came under police investigation on suspicions of receiving bribes from a conglomerate and a notorious swindler.
Kim Kwang-joon was arrested for receiving a total of nearly 900 million won (US$826,000) from Cho Hee-pal, the mastermind of South Korea's biggest pyramid scheme, and the Eugene Group, a mid-sized conglomerate, in exchange for influence peddling.
Just days later, it was revealed that a trainee prosecutor had allegedly engaged in inappropriate sexual conduct with a female suspect he was questioning, at his own office.
The 30-year-old junior prosecutor surnamed Jeon is accused of having sexual activity with a 42-year-old female suspect while questioning her about a theft case on Nov. 10. He is also suspected of having sex with the suspect at a motel two days after their first exchange.
In an aim to overcome the crisis, Han previously said he will look at all options for a new starting point, including the disbandment of the Central Investigation Unit (CIU) under the Supreme Prosecutors' Office (SPO) that handles all high-profile cases.
Also, the SPO has launched an internal inspection into Choi Jae-kyong, the head of the CIU, on suspicion that he advised Kim Kwang-joon on how to deal with the media while Kim was under investigation by special prosecutors.
The inspection, however, has aggravated the internal strife among the prosecution officials, as a group of high-ranking prosecution officials demanded Han voluntarily step down.
Other reform measures include creating an independent investigative body to probe corruption among relatives of the president and senior government officials, officials said.
The prosecution was also mulling over making an independent counsel a permanent fixture instead of on a case-by-case basis, they said.
The prosecution's exclusive right to indict, which is always a source of criticism and debate, is also under review, as the outgoing chief prosecutor was planning to gradually adopt a jury system in the indictment process.
Choi Jae-kyong, the head of the CIU, also said he will soon resign from his post.
Justice Minister Kwon Jae-jin also offered an apology on Friday over a series of corruption incidents involving the prosecutors that eventually led to the chief prosecutor's resignation.
"As the justice minister who commands the prosecution, I feel deeply responsible and offer my apology," Kwon said in a statement, adding that the prosecutors should fairly carry out their work without being swayed.
Meanwhile, the prosecutors supported Han's decision to leave and also vowed to stay humble.
"Since he (Prosecutor General Han) apologized for the two incidents, it is time for the rest us to stay humble, and have time for self-restraint and self-reflection," a Seoul senior prosecutor said, requesting anonymity.
Regarding Han's last-minute decision to scrap the reform measures, another junior prosecutor said, "The prosecutor general made the right decision."
"We should not reform the prosecution hastily," he said. "The prosecution reform measures should be discussed during the next administration, after carefully listening to the voices of the people."