Haruko Obokata, 30, would withdraw two papers at the centre of the controversy, suggested a spokeswoman for Riken, the respected research institute that sponsored the study, marking a steep fall from grace for the young researcher.
"We confirmed that she agreed to retract both articles," the spokeswoman said.
She added that Riken was "still discussing" a retraction with co-author Charles Vacanti of Harvard University.
Obokata was feted after unveiling findings that appeared to show a straightforward way to re-programme adult cells to become stem cells -- precursors that are capable of developing into any other cell in the human body.
Identifying a readily manufacturable supply of stem cells could one day help meet a need for transplant tissues, or even whole organs, meaning that any advance in the field is usually met with excitement in the scientific community.
The study was front-page news in Japan, but within weeks of Obokata's paper on so-called Stimulus-Triggered Acquisition of Pluripotency (STAP) cells being published, questions began to emerge, with fellow scientists saying they could not replicate her results.
Riken had urged the scientist to withdraw her two papers, after concluding that she fabricated at least some of the data.