"I sincerely apologize to the people for creating a shock and disappointment," Hwang told reporters as he was leaving his office at the university. "With an apologetic heart ... I step down as professor of Seoul National University."
Earlier on Friday, a university panel of investigators said Hwang's fabrication was a deliberate deception that has undermined the credibility of science.
The university's announcement of results so far in its investigation into Hwang's work were the first confirmation of allegations that have cast a shadow over all of his purported breakthroughs in cloning and stem-cell technology.
"This kind of error is a grave act that damages the foundation of science," the panel said.
The South Korean government, which had strongly supported Hwang and designated him the country's first "top scientist," said Friday it was "miserable" over the reported results of the investigation and will start its own probe over ethics breaches.
Choi Seong-sik, vice minister of science and technology, said it is impossible to recover money already spent for Hwang, a total $39.9 million for research and facilities since 1998. But his ministry, which admitted errors in its handling of Hwang's projects, will look at ending other funding and withdrawing the "top scientist" designation.
In a May paper published in the journal Science, Hwang claimed to have created 11 stem-cell lines matched to patients in an achievement that raised hopes of creating tailored therapies for hard-to-treat diseases. But one of his former collaborators last week said nine of the 11 cell lines were faked, prompting reviews by the journal and an expert panel at Seoul National University, where Hwang works as a professor.
The panel said Friday it found that "the laboratory data for 11 stem cell lines that were reported in the 2005 paper were all data made using two stem cell lines in total."
To create fake DNA results purporting to show a match, Hwang's team split cells from one patient into two test tubes for the analysis - rather than actually match cloned cells to a patient's original cells, the university said.
"Based on these facts, the data in the 2005 Science paper cannot be some error from a simple mistake, but cannot be but seen as a deliberate fabrication to make it look like 11 stem-cell lines using results from just two," the panel said.
"There is no way but that Professor Hwang has been involved," the university's dean of research affairs, Roe Jung-hye, told a news conference. He said Hwang "somewhat admits to this."
However, Hwang maintained on Friday that he had still created the technology to create patient-matched stem cells as he had claimed in the May article in Science.
"I emphasize that patient-specific stem cells belong to South Korea and you are going to see this," Hwang said.
The investigating panel said DNA tests expected to be completed within a few days would confirm if the remaining two stem-cell lines it had found were actually successfully cloned from a patient.