Does time spent in Japan via the U.S. military's SOFA agreement count towards naturalization?

Contrary to popular belief, the "Y" on these
license plates doesn't mean "Yankee". ☺

The United States and Japan, like many other countries, have a special treaty called the "Treaty of Mutual Cooperation and Security between the United States and Japan" (日本国と {Nipponkoku to}​アメリカ合衆国との間の {Amerikagasshūkoku to no Aida no}​相互協力及び {Sōgo Kyōryoku oyobi}​安全保障条約 {Anzen Hoshō Jōyaku}), known as the 安保条約 {anpo jōyaku} or even just 安保 {anpo} for short. It's a long and complicated (and controversial) treaty that has been in place and renewed since 1960.

Part of the provisions of the treaty allow for the U.S. military to bring in and rotate tens of thousands of U.S. military (and civilian) personnel in and out of Japan, living on or near military bases.

Because so many U.S. citizens (almost as many as U.S. nationals that live in Japan as a standard foreign resident) move in and out of Japan, serving the U.S. military, the U.S. military has crafted an agreement with Japan's MoFA (外務省 {gaimushō}) which allows Americans serving the U.S. military in Japan to bypass almost all of the procedures related to obtaining status and permission to live in Japan as a foreign resident.

U.S. military and some civilians serving them who are posted in Japan do not need a visa to enter Japan. Some do not even need a passport! In fact, some young soldiers do not have one.

The CAC, similar to Japanese domestic ID,
has a smart-chip, 2D code & RFID.

A U.S. military I.D. and proper order papers is all they need to enter and stay in Japan (though it should be noted that where they can be and what they can do is dictated and controlled strictly by the U.S. Armed Forces) To drive, they do not need a Japanese driver's license — their cars have special license plates with the Latin letter prefix "Y" on them (which means "Yokosuka", the location of a large base, though you will see these cars near all bases such as those in 沖縄Okinawa even though they're nowhere near 神奈川県横須賀市Kanagawa-ken Yokosuka-shi (Yokosuka City, Kanagawa Prefecture).

This agreement is known as the SOFA (地位協定 {chiikyōtei}).

Of course, there are some in the U.S. military that come to love Japan and have either stayed here so long or developed or had ties to the country that they want to stay in Japan after their service to the U.S. Armed Forces is over. And there are some who even want to naturalize. A person in Okinawa recently asked us if the time spent in Japan via the SOFA counts towards the required physical residency condition — either five (5), three (3) or one (1) consecutive year(s) depending on whether it's regular naturalization or simplified naturalization.

The answer for this person, unfortunately, is sorry, but no: because people staying in Japan via the SOFA bypass all the requirements and checks for acquiring and staying in Japan via a regular visa or SoR (在留資格 {zairyū shikaku}), there is explicit language in the SOFA agreement that says that it doesn't entitle the person to have any expectation of being able to live in Japan permanently or even to live medium to long term as a normal foreign resident of Japan. The legal language in the agreement is as follows:

ARTICLE Ⅸ

2. Members of the United States armed forces shall be exempt from Japanese passport and visa laws and regulations. Members of the United States armed forces, the civilian component, and their dependents shall be exempt from Japanese laws and regulations on the registration and control of aliens, but shall not be considered as acquiring any right to permanent residence or domicile in the territories of Japan.

And in Japanese:

第九条

2. 合衆国軍隊の構成員は、旅券及び査証に関する日本国の法令の適用から除外される。合衆国軍隊の構成員及び軍属並びにそれらの家族は、外国人の登録及び管理に関する日本国の法令の適用から除外される。ただし、日本国の領域における永久的な居所又は住所を要求する権利を取得するものとみなされない。

Even if somehow the ministry did allow time spent in Japan via the SOFA to count towards one's physical residency requirement for naturalization, it'd be extremely difficult to prove it. Because no records are made of entrances and exits to Japan in either a passport or in Japan's immigration computer databases, calculating and proving that a candidate spent the required amount of time in Japan would be extremely challenging, if not impossible.

In summary, people who spend time in Japan with the military without having obtained a regular will need to apply for a regular visa and earn their time here as a regular foreign resident via a standard foreign civilian SoR (在留資格 {zairyū shikaku}) issued by the MoJ (法務省 {hōmushō}). In contrast, time spent in Japan as a student under a student visa, contrary to what you might read on the internet, does count as foreign residency, although it is unlikely that a student fresh out of school will meet the guidelines regarding being able to show that they established a stable financial situation in Japan enabling them to live there relatively little difficulty.

Finally, a word of caution to U.S. military considering changing their nationality to Japanese: some financial and/or other benefits that the U.S. Armed Forces provides to retired personnel may be forfeited in you voluntarily give up your U.S. citizenship (a requirement for naturalization to Japan). I don't know if "relinquishing" one's U.S. nationality instead of "renouncing" one's nationality counts as "voluntarily" in the eyes of the U.S. military; I would recommend consulting with qualified U.S. military legal advisers regarding this.