The revelations come a week after a young researcher at the centre of the scandal, which has rocked the country's scientific establishment, said she would resign after failing to reproduce the successful conversion of an adult cell into a stem cell-like state, known as "STAP" cells.
The failure marked a stunning fall from grace for 31-year-old Haruko Obokata, whose co-researcher committed suicide amid the embarrassing scandal that prompted respected science journal Nature to retract an article detailing the research.
"But we can't conclude whether the mixing was done on purpose or by mistake nor can we conclude who did it," probe team chief Isao Katsura, head of the National Institute of Genetics, told a news briefing in Tokyo.
In January, Riken trumpeted Obokata's simple method to re-programme adult cells to work like stem cells.
The study was top news in Japan, where the photogenic Obokata, a Harvard-trained scientist, became a phenomenon.
Mistakes were discovered in some data published in two papers, photograph captions were found to be misleading, and the work itself could not be repeated by other scientists.
The head of the probe team, which was made up of scientists outside the institute and lawyers, today said the committee interviewed Obokata three times.
"During the last of our interviews we told her that we had enough evidence to show the mixing-in (of embryonic stem cells)," Katsura said.
"Then, before us asking anything, Ms.Obokata said 'I've never mixed them.
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