It is possible in Japan to complete the entire tax return filling and payment online. This solution may be very useful for a company headquartered abroad. There is however one important precondition to using online tax-services, which prevents foreign companies from using the online portals: 

Companies must have legal residence in Japan, which is necessary to obtain a digital ID/Electronic certificate.

e-Tax

www.e-tax.nta.go.jp

e-Tax is the National Tax Agency’s online tax website. A company will able to file tax returns and pay national Corporation taxes on this website. 

eLTAX

https://www.eltax.lta.go.jp/

eLTAX is the equivalent for local taxes. There is no information in foreign languages available