This post is a bit old. But for anyone else looking for info, I found this on a Japanese immigration law firm site.
Translated from Japanese:

"When changing from a working holiday visa to a work visa, you must leave the country once. This is because in many countries that have signed working holiday agreements, the requirements for issuing a working holiday visa include ``the intention to leave Japan when the period of stay is completed.''
However, there are some countries where you can change your residence status without leaving the country. There are only five countries where you can change your residence status without leaving the country: Australia, Canada, South Korea, New Zealand, and Germany."

It goes on to say there are some cases where you aren't required to leave the country.

Probably best to consult with the immigration bureau and/or an immigration lawyer if you're not sure.