Most of the ministry’s posts in charge of personnel evaluation are held by men, which means promotions are decided from the viewpoints of men. That puts women at a disadvantage.

What were the reasons for passing her over?

Most of the ministry’s posts in charge of personnel evaluation are held by men, which means promotions are decided from the viewpoints of men.

And this is a surprise to anyone?

Yup. My g/f works at a very traditional Japanese company where only the men are given promotions. I kid you not - a junior male joined the company and was promoted within 12 months. Meanwhile, a number of female staff who've been there several years get nothing. Anecdotal - sure - but I bet this happens everywhere...