Are you sure that you are a "Special Permanent Resident?" That is the status for the "zainichi" people (mainly Korean but also some Taiwanese and a handful of others) left over in Japan after WWII and their descendants, who are not citizens but have an indefinite leave to be in the country. It is different from being a regular "Permanent Resident" (someone who came to Japan on a fixed-term visa and converted it to PR). Regular "Permanent Residents" only get one year, just like everyone else.

(I avoided talking about the old re-entry permit system above because it would get confusing in the context of the question. But yes, it was a pain in the butt -- unless you could afford to outsource the application to a third party, which my employer kindly did...)