It said it would consider retroactively admitting those who otherwise would have passed the exams, although it did not explain how it would do so.
One of Japan's most prestigious medical training schools has admitted marking down female applicants' entrance exams to maintain a majority of men in each year.
The scandal was uncovered by investigators looking into claims the university padded the scores of an education ministry bureaucrat's son to help him gain admission, and local media said other instances had been discovered where individual entrance test scores were revised upwards, suggesting favouritism.
Last month, prosecutors indicted the two top executives at the university on bribery charges.
The investigation found that in this year's entrance exams the school reduced all applicants' first-stage test scores by 20 per cent and then added at least 20 points for male applicants, except those who had previously failed the test at least four times.
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It said the school wanted fewer female doctors because it anticipated they would shorten or halt their careers after becoming mothers.
The scores of six applicants including the son of Futoshi Sano, 59, a former senior education ministry official, were inflated by up to 49 marks in this year's primary exam with a maximum score of 400, the sources said.
The manipulation was "nothing but discrimination against women", said one of the lawyers hired by the university to investigate the alterations, speaking at a press conference on Tuesday. We want to sincerely apologise for this", Tokyo Medical University managing director Tetsuo Yukioka told reporters as he bowed deeply. He denied any previous knowledge of the score manipulation and said he was never involved.
Mr Yukioka said women were not treated differently once they were accepted, but acknowledged that some people even believed women were not allowed to become surgeons.
Recent reports have revealed that the medical school's written admission test is deliberately discriminatory against women, working on a points system where men could score a full 100 and women can only reach 80 out of 100.
It is understood the practice of subtracting points from female candidates was done to prevent a shortage of doctors at affiliated hospitals, as some at the medical college believed that female doctors tended to resign or take long periods of leave after getting married or giving birth.
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