The report said that scores of female applicants were slashed by about 10 per cent.
Such alterations "should never happen", added Keisuke Miyazawa, vice president of the university, pledging next year's entrance exams would be fair without giving further details.
The scandal was discovered during an investigation into the admission of a ministry official's son, who has now been charged, with his father, for allegedly securing favourable treatment in exchange for funds. The findings released Tuesday by lawyers involved in the internal investigation confirm recent reports in Japanese media.
The lawyers also attested that all entrance examination scores for women were deducted, as ordered by Usui and with the knowledge of Suzuki and another senior official at another renown university, to prevent a shortage of doctors at the university's affiliated hospitals.
A Japanese medical school deliberately cut women's entrance test scores for several years, a panel of lawyers hired by the school to investigate the issue said on Tuesday, calling it a "very serious" instance of discrimination.
The practice had reportedly been going on for more than a decade.
The investigative report said the manipulation was "profound sexism", according to lawyer Kenji Nakai.
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In Japan, women are highly educated, but the intensity of work habits, which can lead to deaths due to overwork, often leads women to stop their careers when they start a family. Those of all women, and men who had failed the test at least three times, were not, however.
"The world's getting more equal than in the past, but we are still looked down upon as women", university student Yumi Matsuda said.
In the second and final test stage, just 2.9 percent of female applicants were admitted, compared with 8.8 percent of male applicants.
Around 2006, executives at Tokyo Medical University saw what they thought was a problem with their applicants: Too many women. Kyoko Tanebe, an obstetrician and a director of the Japan Joint Association of Medical Professional Women, pointed to doctors' workstyle presupposing "selfless devotion" and long working hours as sources of the problem.
Prime Minister Shinzo Abe has made a priority of creating a society "where women can shine", but women in Japan still face an uphill battle in employment and face hurdles returning to work after childbirth, a factor behind a falling birthrate.