You need a visa for South Sudan if you have a Japanese passport
Visa options for South Sudan
Electronic visitor visa
Travellers need a visa to visit South Sudan for Business or Tourism. An eVisa is the fastest and easiest way of obtaining a visa for South Sudan because travellers can submit their application and supporting documents online. Once the application is approved, travellers receive their eVisa confirmation electronically. A valid visa is required to board the flight. If the visa is expired or doesn’t match the traveller’s passport information, travellers will not be able to board their flight.
This is not offered by sherpa°.
Apply on the government site.