Dr Hwang has apologised for fabrications in his work |
A spokesman for South Korea's state auditors said Dr Hwang was questioned over potential misuse of public funds.
Dr Hwang and his team received more than $40m for his work with stem cells, in the hope that his landmark research would help cure a range of diseases.
Dr Hwang has already apologised for flaws in his research.
However, the scientist has insisted that most of the fabrications were carried out without his knowledge, by collaborators on the project.
Dr Hwang was being questioned at Seoul National University, where he was a professor.
"An investigation is under way into the appropriateness of Hwang's use of the money," said an official at the Board of Audit and Inspection (BAI), according to the Yonhap news agency.
Any evidence of financial wrongdoing would be passed on to prosecutors who are conducting a separate investigation into the case, a BAI spokesman told the AFP agency.
Dr Hwang and his team could include charges of fraud and embezzlement if he is found to have faked his research to ensure its funding.
A final report on the scandal from experts at Seoul National University, published earlier this month, said that Dr Hwang had faked both his most famous research papers.
A final report from experts at Seoul National University, published earlier this month, said that Dr Hwang had faked his most famous work, the production of a stem cell line taken from cloned embryos.
The panel had previously rejected another of his landmark claims - to have produced individually tailored stem cells.
But it did conclude that Dr Hwang produced the world's first cloned dog, an Afghan hound called Snuppy.
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