An internal investigation found that Tokyo Medical University (TMU) had been manipulating the scores of female applicants from as early as 2006.
It also marked down the scores of male applicants who had taken the entrance test at least four times.
TMU has said the alterations should never have happened.
The university also admitted to adding extra points to the scores of 18 students who had made donations to the school.
"We betrayed the public trust. We want to sincerely apologise for this," TMU managing director Tetsuo Yukioka told reporters at a press conference on Tuesday.
Keisuke Miyazawa, vice-president of TMU also pledged that next year's entrance exams would be fair.
The story was first reported last week by Yomiuri Shimbun, the country's biggest daily paper and has since sparked national outrage.
The report had quoted an unnamed source saying officials adopted a "silent understanding" to reduce the number of female entrants over concerns female graduates were not going on to practice medicine in employment.
"Many female students who graduate end up leaving the actual medical practice to give birth and raise children," the source told the newspaper.
In 2010, before the measure was allegedly introduced, female student participation was about 40%.
The newspaper reported that after the two-round application process earlier this year, only 30 female applicants were accepted to study, versus 141 men.