Apply for a passport as soon as you receive an acceptance letter from Nagoya University.
Nagoya University will apply for a COE to the local immigration bureau on your behalf. A COE will be issued in a digital format via email. Nagoya University will forward the email (electronic COE) upon issuance. The COE is valid for 3 months after the date of issue and you must enter Japan before the COE expires.
Apply for a visa with your nearest Embassy of Japan (or Consulate-General of Japan). You need to present the COE (email) on your smartphone or a copy of the email. Please check with the embassy (or consulate) in advance regarding the procedures since the process and necessary documents are different for each country.
At the airport where you arrive, you will present your passport, visa and the COE (email). The immigration officer will grant you "landing permission" by affixing the seal in your passport. If you land at Narita, Haneda, Kansai, Chubu airport, etc. and are granted a period of stay is longer than 3 months, a Residence Card will be issued. Those who received a Residence Card can apply for a part-time work permit, which is called "Permission to Engage in Activity other than That Permitted under the Status of Residence Previously Granted". Those who wish to apply should ask the Student Affairs Division of your school for details well in advance. (You can also apply for this permission at a later date.)