Hwang will be stripped of his Order of Science and Technology Merit Changjo Medal in July, said Min Jin-kee, an official in charge of the issue at the Ministry of Government Administration and Home Affairs.
The 52-year-old scientist was indicted last month for allegedly accepting US$2 million in private donations based on the outcome of falsified research and embezzling about US$834,000 in private and government research funds.
If convicted, Hwang faces at least three years in prison, which could also see him lose another honor, the Order of Service Merit Red Stripes, Min said.
Last year, the South Korean government revised a law so that those convicted of major crimes can be stripped of their state honors, the AP reports.
Hwang has admitted inflating data for key research papers published in 2004 and 2005, but blamed other researchers for deceiving him with falsified research results.