Such alterations "should never happen", added Prof Keisuke Miyazawa, vice president of the university, pledging next year's entrance exams would be fair without giving further details.
The sexist practice was uncovered during another investigation on the same university's ethics, as it is also accused of favoring the son of an influential member of the Ministry of Education by admitting him to the school without the required grades, according to the Japanese paper.
A major score-rigging scandal has engulfed one of Tokyo's medical schools, with an investigation revealing the university deliberately marked down all female applicants to limit the number of women studying at the school.
The sources also said that there were examination invigilators at the university that used a specific manual to guide the process of manipulating students' points to control the enrollment process. The lawyers' report is expected to be released on Tuesday afternoon.
In addition, they confirmed the practice of subtracting exam points for all women, as well as for men who were taking the test for at least the fourth time.
The investigation showed the scores of men - including those reappearing after failing once or twice - were raised a certain number of points.
"This incident is really regrettable - by deceptive recruitment procedures, they sought to delude the test takers, their families, school officials and society as a whole", lawyer Kenji Nakai told a news conference.
One of the lawyers, who had been conducting an internal probe into the university's practice of tampering with examination results and allowing "backdoor" admissions to some students in return for favors, said the practice was discriminatory.
In 2018, the ratio of women accepted to the medical school after the first round of tests was 14.5 per cent, compared with 18.9 per cent for men. 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.
Around 2006, executives at Tokyo Medical University saw what they thought was a problem with their applicants: Too many women.
Prime Minister Shinzo Abe has made "womenomics" - or boosting women's participation in the workplace and promoting women to senior positions - a priority, but the pace of progress has been slow.
Entrance exam discrimination against women was "absolutely unacceptable", Education Minister Yoshimasa Hayashi told reporters last week.