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.
A Tokyo medical school apologized Tuesday after an internal investigation confirmed that it altered entrance exam scores for years to limit the number of female students and ensure more men became doctors.
The school said the manipulation should not have occurred and would not in the future.
Initial reports suggested the practice dated to 2011, but a probe conducted after the reports found the alterations started as early as 2006, Kyodo News reported Tuesday.
"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.
It also showed the scores of men - including those reappearing after failing once or twice - were also raised by at least 10 points.
The university also disliked accepting male applicants who had failed a number of times because they also tend to fail the national exam for medical practitioners, which would bring down the university's ratio of successful applicants and hurt its reputation, according to the sources.
The lawyers said they did not know how many women had been affected.
The lawyers' report also revealed that executives also padded the scores of some applicants of former graduates so the university could commandeer more donations from their parents.
One of the reasons cited for excluding women was the suggestion that female doctors can't work long hours after getting married or having children.
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.
Women's empowerment minister Seiko Noda told Japan's NHK public broadcaster the exam points manipulation had been "extremely disturbing".
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