Under the current measures, everyone, including those from visa-exemption countries, has to apply for a visa, but the procedure is quite simple. The only document you need (in addition to the usual application materials if you are from a non-visa-exemption country) is the certificate issued by the system called ERFS, which will be applied through the ICRR. So when you plan your visit, please send e-mail to nnn2022-visa@km.icrr.u-tokyo.ac.jp to start visa procedures. The whole process of obtaining a visa usually takes only a week or two, but please start the preparation as early as possible.