A Japanese medical university has systematically discriminated against female applicants because women tend to quit as doctors after starting families, media reports have alleged.

The Yomiuri Shimbun newspaper said Tokyo Medical University had manipulated the entrance exam results of women since about 2011 to keep the female student population low. Quoting unidentified sources, it said the manipulation started after the proportion of successful applicants who were women reached 38% in 2010.

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Other Japanese media, including NHK and Kyodo News, also reported claims of exam manipulation. Quoting unnamed sources, NHK said female applicants’ scores were slashed by about 10% in some years.

The allegation surfaced during the university’s investigation of a separate scandal in which its former director was accused of granting admission to the son of a senior education bureaucrat in exchange for a favour.

The school’s public affairs department said officials were surprised by the Yomiuri Shimbun report and had no knowledge of the reported manipulation. It promised to look into the matter.

Yoshiko Maeda, the head of the Japan Medical Women’s Association, said it was astonishing that women were being stripped of their right to seek entry to the medical profession.

“Instead of worrying about women quitting jobs, they should do more to create an environment where women can keep working,” Maeda said in a statement on the association’s Facebook page. “And we need working-style reform, which is not just to prevent overwork deaths but to create a workplace where everyone can perform to the best of their ability regardless of gender.”

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In Japan, many female graduates face discrimination in hiring and pay. Long working hours and lack of support in child-rearing from their husbands often force them to give up their careers. As Japan’s population ages and birth rates remain low, many workplaces including hospitals are chronically short-staffed.

This year a health, labour and welfare ministry panel urged medical institutions to allow more flexible working environments and support for female doctors so they could return to work after maternity leave and balance work and family.

Women account for more than 40% of the overall workforce, but the share of female doctors who have passed the national medical exam has been stuck at about 30% for more than 20 years. The slow progress in medicine has prompted speculation among some doctors about possible widespread interference in the school admissions process.

The education minister, Yoshimasa Hayashi, said: “Entrance exams that unfairly discriminate against women are absolutely not acceptable.” He said the ministry would decide on its response after receiving the results of an investigation from the school.

In Japan, medical graduates usually end up working at school-affiliated hospitals. According to the Yomiuri Shimbun, the Tokyo school started to restrict the proportion of women in each class to about 30% by manipulating test scores thereby failing more women.

Admissions records released to the Associated Press by the school show the percentage of women who passed the entrance exam rose from 24% in 2009 to 38% in 2010. The figure has since stayed below that level, falling to 18% this year. The percentage of female applicants who were accepted this year was 2.9%, compared with 8.8% of male applicants.