The Education Ministry sent a questionnaire to all medical schools asking them for six years of data on the genders and ages of all applicants, those who passed the entrance exam and those who were admitted.
The questionnaire also asks if the schools took the precaution in this year's exam of masking the IDs of applicants including their names, ages and genders in deciding whether they passed.
The ministry set a deadline of Aug. 24 for responses.
A Tokyo medical school released an internal investigation earlier this week that confirmed media reports that it had altered entrance exam scores to limit the number of female students. Tokyo Medical University said it believed female doctors would shorten or halt their careers if they had children, affecting hospital staffing.
Medical graduates in Japan usually work at school-affiliated hospitals after completing their training.
Education Minister Yoshimasa Hayashi told a news conference Friday that the rigging of scores at Tokyo Medical University was "extremely inappropriate and a serious matter that eroded trust in universities," according to Japan's Kyodo News service.
The manipulation came to light during an investigation into allegations that the school admitted the son of an education ministry official in exchange for favorable treatment for the school in obtaining research funds. The bureaucrat and the former head of the school have been charged with bribery.
The investigation found that the school reduced all applicants' first-stage test scores by 20 percent this year and then added at least 20 points for male applicants, unless they had failed at least four times previously.
"We sincerely apologize for the serious wrongdoing involving entrance exams that has caused concern and trouble for many people and betrayed the public's trust," school managing director Tetsuo Yukioka said. He denied any previous knowledge of the score manipulation and said he was never involved.
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