Hwang was also charged with embezzlement and with illegally paying for human eggs to conduct his research.
If convicted on the fraud charge, the former Seoul National University professor could face up to 10 years in prison.
He was sacked by the university after admitting he fabricated data in two high-profile scientific papers published in 2004 and 2005.
Hwang recieved global acclaim and was often called "the pride of Korea" at home after his team said it had achieved three milestones that put the country at the centre of stem cell research.
The papers raised hopes that stem cells – undeveloped cells that can potentially grow into different kinds of tissue - could be used to treat diseases such as Alzheimer's.
Prosecutors announced the charges at a nationally televised news conference.
They said that Hwang had falsified his findings but that "there has been no precedent in the world" for prosecuting those who carry out fraudulent scientific research.
Supporters of Hwang Woo Suk
weep after charges are announced
He was charged with accepting two billion won ($2.1 million) in government funding based on the outcome of the fabricated studies.
Prosecutors say that Hwang also embezzled about 800 million won ($856,000) in private and government research funds
Five members of his research team were charged with obstruction of duty, fraud and for violating South Korean bioethics laws.
Hwang has said he is the victim of a conspiracy to discredit him and has blamed junior researchers at a fertility clinic that took part in the research for the fake data.