Prosecutors are already probing Hwang for possible fraud in connection with his research funding.
The Board of Audit and Inspection (BAI) said in a report that Hwang had failed to account for 6.2 billion won ($6.4 million) in donations for his research - one billion won in state funds and 5.2 billion won in private donations.
Auditors said they would refer his case to the prosecution after concluding that Hwang kept millions of dollars in donations in his personal bank accounts of which more than $6 million had simply disappeared.
"There was no way to verify its use," senior BAI official Park Eui-Myong told a press conference in Seoul on Monday, in reference to the missing part of the research fund.
"We are planning to refer all the data on what Hwang misappropriated or used for unclear purposes to the prosecution."
Hwang's team received a total of 37 billion won in research funds over the past five years and spent 25 billion won. Of that some 6.2 billion won was spent in unaccounted ways.
Hwang, 52, was lionized as a national hero here after he stunned medical experts in 2005, claiming to have created 11 patient-specific stem cell lines.
But his fall from grace came swiftly at the end of last year and has been gathering momentum since last month when a scientific verification panel found he had created no stem cells of any kind and that his research data was fabricated.
"We are planning to refer all the data on what Hwang misappropriated or used for unclear purposes to the prosecution"
Senior BAI official
In a series of damaging revelations about Hwang, the National Bioethics Committee said last week he had lied about eggs from his junior researchers.
The committee said Hwang had forced two of his junior researchers to give eggs for his stem cell research, contrary to his earlier denials of forcing any of his staff to contribute eggs.
Prosecutors have questioned co-authors of Hwang's research, while the respected US journal Science has retracted his papers.
Prosecutors confirmed last month that Hwang never created stem cells tailored to individuals as he had claimed in a 2005 scientific paper.
Stem cells are master cells that have the potential to develop into any organ of the body. Scientists believe the cells can be used to fight a range of diseases including cancer, diabetes and Alzheimer's.