The scientist, Dr. Hwang Woo Suk, and five members of his research team were indicted, a prosecution official, Lee In Kyu, said at a nationally televised news conference.
Dr. Hwang was hailed as a global stem cell pioneer and treated as a national hero until investigations late last year showed that he had fabricated key data in two papers published in the journal Science.
He was later fired from his post as a professor at Seoul National University, where he did his research.
Government auditors said in February that it was unclear how he had spent $2.6 million of the $33 million in government funds and $6.4 million in private donations he received.
He claimed to have created the world's first cloned human embryos and extracted stem cells from them, raising hopes of cures for diseases like Alzheimer's and Parkinson's.
He later apologized for inflating data, but accused other researchers of deceiving him with falsified results. He says he has the technology to do what he claimed, but the Health Ministry has blocked his research.