• Get a Hanko
• Write a business profile
• Find an accountant to handle paperwork
• Find a public notary (gyosei-shoshi) to register the company for you
• Open a corporate bank account
• Register an address with the post office

Read relevant material

• National Tax Agency guidelines for notification of starting a business

File with a local tax office

Register as a Kojin Jigyo (個人事業).

File a Notification of Commencement of Business form (kojin jigyo no kaihaigyo todokedesho, 個人事業の開廃業等届出書).

File at a local tax office

with the  ( “”) http://www.nta.go.jp/tetsuzuki/shinsei/annai/shinkoku/pdf/04.pdf
Submit to  local tax office (see the “「所在地及び管轄」” (shozaichi oyobi kankatsu–[tax office] locations and jurisdictions listed here http://www.nta.go.jp/soshiki/kokuzeikyoku/kankatsukuiki/syozaiti.htm

館林     〒374-8686
館林市仲町11番12号     0276-72-4373
自動音声でご案内します     太田市　館林市 邑楽郡     0241

Pay taxes using the 青色申告 aoiroshinkoku blue form http://www.nta.go.jp/tetsuzuki/shinsei/annai/shinkoku/pdf/09.pdf

:  income tax (shotoku-zei), sole proprietor tax (kojin jigyo-zei) and residential tax (jumin-zei)
Need to keep good records (single-account bookkeeping gets 100,000 deduction, double-account bookkeeping gets 650,000 deduction)

Consider hiring a and an accountant for paperwork
Public Notary

Tokyo Business Center http://www.seisakukikaku.metro.tokyo.jp/invest_tokyo/english/business-support/one-stop.html