For Hiroko (not her real name), discovering she'd failed to get into Tokyo Medical University twice after years of hard work left her devastated.

Key points: TMU systematically and deliberately marked down all female applicants to limit the number of women studying at the school

TMU systematically and deliberately marked down all female applicants to limit the number of women studying at the school The ministry's investigation of 81 medical schools found some had boosted scores of children of former alumni

The ministry's investigation of 81 medical schools found some had boosted scores of children of former alumni Japan's Prime Minister has spruiked the importance of women in the workplace, but the country has just 20 per cent female doctors

"I thought I might not make it again this year, my future is completely dark and I couldn't see ahead," she said.

But once she found out she might have failed the entrance process just because she was a woman, her disappointment turned into white-hot anger.

A Tokyo Medical University (TMU) internal investigation revealed it had systematically and deliberately marked down all female applicants to limit the number of women studying at the school.

It is understood senior TMU officials wanted to keep the ratio of women to men at 30 per cent because they believed women would take long periods of leave after childbirth and marriage, leaving the country with a doctor shortage.

"I felt the professors … considered female students only as a number and didn't think of each student's effort, pain and life at all," Hiroko told the ABC.

The TMU's revelations sparked an education ministry investigation into the sector that found more Japanese universities were likely to have manipulated results against women.

Since then, the scandal has snowballed.

TMU systematically and deliberately marked down female applicants. ( ABC News: Yumi Asada )

The ministry's investigation of 81 medical schools found some had boosted scores of children of former alumni, selected applicants from a waiting list outside of the order of results and deducted points from applicants who had failed in the past.

Juntendo University had the highest gap between male and female pass rates. In the most recent exams this year, 10 per cent of men and 5 per cent of women passed.

University officials previously denied that they were discriminating against women or former applicants, but that they and the education ministry interpret the use of "discretion" differently.

Medical student Yui Yamamoto applied to Showa University, which admitted to giving preferential treatment to children or relatives of alumni — but denied gender discrimination.

"It's unforgivable to shut out excellent people during the exams," she told the ABC.

"My friend was asked during an admission interview, 'what do you think you'll do when you get married and get pregnant?'"

"There are no men who were asked that question."

Despite failing the TMU exams and the subsequent emotional low, Hiroko turned her disappointment around and is now studying at a prestigious public medical school.

Medical student Yui Yamamoto, who applied to Showa University, said it was "unforgivable to shut out excellent people". ( ABC News: Yumi Asada )

But the experience at TMU still has her worried about her future as a medical professional.

"I'm very scared that there will be some kind of repercussion during hospital recruitment … after I graduate from university," she said.

"It's because the doctors' world is very small and there are still many doctors who think that female doctors are no good.

"[During my interviews] it was a matter of course to ask [discriminatory] questions — and it was written in a book on how to prep for interviews.

"I remember memorising the answer, 'I will work my whole life as a doctor even after I have a baby and raise a child.'"

'Japan still makes decisions on baseless reasons'

For urologist Doctor Yoshiko Maeda, the scandal is a sign of how behind Japan is when it comes to gender equality.

Dr Maeda also runs the Japan Medical Women's Association.

"I was so angry because Japan still makes decisions on baseless reasons like the fact that women can't do things just because they're women," she said.

"Japan is a very male-dominated society so even after women become doctors there is always gender bias — such as discrimination against women — and it probably gets harder as they get older."

The OECD's latest statistics on gender equality in the health sector shows Japan ranks the worst when it comes to the share of female doctors, at just 20 per cent.

For doctor Yoshiko Maeda, the scandal is a sign of how behind Japan is when it comes to gender equality. ( ABC News: Jake Sturmer )

To compare, Australia stands at 39.4 per cent.

"People are trying to get rid of discrimination all over the world, but Japanese society can't eliminate strong prejudice," Dr Maeda said.

"This is despite the Prime Minister [Shinzo Abe] having a policy for increasing women's workplace participation.

"It's very sad."

Japan's Prime Minister spruiked the importance of women in the workplace — a variation on his Abenomics known as 'womenomics'.

While there is still more to come from this scandal, it is hoped that it will at least force the country to confront some hard truths about gender roles in Japan.

Medical school discrimination went beyond gender

But the problems with access to tertiary education weren't just gender discrimination.

Yuzo Takeguchi said he had applied for multiple medical schools dozens of times.

"You have to study seven to eight hours a day — it's almost the same as working full time," he said.

"It costs 60,000 yen ($720 AUD) to take one exam at each university — I tried 10 to 12 universities every year.

"It took me over two years to enter a medical university. It became financially difficult when I didn't pass the exam and it was a tough situation as I tried to challenge it again while working somewhere else."

The education ministry's investigation revealed that some universities were penalising students who had sat — and failed — the test multiple times.

Yuzo Takeguchi eventually succeeded and is currently studying medicine at Fukushima Medical University.

Medical student Yuzo Takeguchi sat dozens of entrance examinations and believes he was secretly being marked down for taking the exam multiple times. ( ABC News: Jake Sturmer )

But he believed he had been a victim of this scandal — and is demanding transparency.

"I want the universities to disclose exactly what happened. The damage is not clear without disclosure of the information and it won't stop it from happening again in the future," he said.

Applicants 'betrayed': Education Minister

Japan's Education Minister Masahiko Shibayama urged all universities to take a look at their selection process before next year's exams.

"I find it deeply disappointing that applicants have been betrayed and social trust in universities has been undermined," he said earlier this year.

The ministry will spend the rest of the year investigating the remaining 51 schools before releasing its final report.

Since the scandal broke, Tokyo Medical University has appointed its first-ever female president.

Sorry, this video has expired Director of Tokyo Medical University apologises for cutting female entrance scores

This week the new president, Yukiko Hayashi, reiterated the school's apology, but would not state whether there was clear gender discrimination because she was not part of the admissions committee at the time.

The school promised to offer 101 students who were unfairly rejected the chance to enrol, but said it would cap the number at 63 students.

Showa University apologised for its "poor execution" of the selection process and vowed to stop manipulating the results.

It set up a panel of experts to examine how to respond.

Juntendo University is expected to address its findings later this month.