The papers were published by a group at the university's Institute of Molecular and Cellular Biosciences led by Shigeaki Kato, a widely known endocrinologist in charge of a national project that was granted more than $200 million in funding between 2004 and 2009.
Kato, who resigned from the institute last year, denied involvement in any falsifications but said in an interview with The Mainichi Shimbun he "would accept the university's decision."
The university said it began an investigation after allegations were made by an outside source.
The university discovered fabricated data including Photoshopped and partially deleted materials in 165 papers published after Kato's arrival in 1996, officials said.
The investigators concluded 43 papers on a range of subjects from fat-cell increases associated with obesity to DNA multiplication through cell division should be retracted, and another 10 needed to be revised.
University officials said they believed Kato wasn't directly involved in falsification of the data but the way he managed the research resulted in misconduct.
Kato said he was in charge of checking experimental results and revising papers.
"I think my team members rushed to obtain successful results," he said. "I'm sorry for troubling the university, the institute, and the science committee and I'm working on retracting the papers."
More than 20 researchers are listed as co-authors of the papers in question.
"The papers damaged the university's social credibility while greatly affecting the future of young researchers," a member of the investigation panel said.