There are many resources available in Japanese. Search for "NPO 設立" in Google or Amazon.co.jp to find numerous websites and books.
As for English resources, this page has quite a bit of information: http://www.gdrc.org/ngo/japan-ngo.html
That page contains a list of information centers that you may have luck with. You can find an older yet more complete list of information centers (with icons to indicate which ones can speak English) here: http://www.jnpoc.ne.jp/English/library/localnpocenter/index....