However, online Yomiuri articles are quickly 'firewalled' so Japan HEO will look for corroborating articles at other sources, such as Kyodo, Japan Times, etc.
The 54% refers to those who finished a PhD and joined the already dismal job market this spring.
In a nutshell, the trends with PhDs in Japan are: (1) most hope to get a post in Japanese academia and/or a government-funded research institute (most of which overlap significantly with academia here), (2) there simply isn't enough growth in jobs to match the increase in PhDs, (3) companies have always been reluctant to hire PhDs (too old, speciality irrelevant, etc.) while they have given up on more and more research due to the two-decade-long bad economy, (4) more and more PhDs have to settle for jobs that do not require a PhD and/or are outside the speciality of the degree holder.
Some background reading is available at these two Nature.com articles:
Scientists to spare
Employing Japan's postdocs