Can you be denied entry into Japan if you're naturalized?

The "No Entry" road sign in Japan
is also the same in much of Europe.

Legally in Japan, there is no difference in the rights between Japanese nationals who were born with the nationality (often called "natural born citizens" in American terminology) and those who changed from one nationality to another voluntarily via a qualifying process (usually referred to as "a naturalized citizen" or national). Some countries may small differentiations between natural born and naturalized citizens. For example, the United States requires U.S. Presidents to be natural born. Some countries make it easier to lose or forfeit their nationality if the nationality was acquired via naturalization (ex. Mexico).

But in Japan, a naturalized person is legally capable of becoming, for example, the Prime Minister. Just like somebody who has only had Japanese nationality their entire life. A naturalized Japanese citizen "commoner" woman could even theoretically become a member of the Imperial Family through marriage. Although it should be pointed out that members of the Royal Family, although Japanese, are questionably not the same as Japanese nationals in that they have less rights than a Japanese citizen: they have no family register (though they are on a special royal register), no passports, they can't vote, they can't run for office, and much of the freedoms we take for granted can only be done with permission by handlers.

So the question isn't really:

"Can you be denied entry into Japan if you're naturalized?"

but rather:

"Can you be denied entry into Japan if you're legally Japanese?"

What happened in April of 2021?

During the height of the COVID19 pandemic in Japan and the world in the spring of 2021, three Japanese nationals attempted to enter Japan: two from the United States, and one from the Netherlands. They arrived via airplane at Narita and Kansai International Airports.

Although they had Japanese Passports, they did not have recognized "coronavirus inspection certificates".

Because of this, rather than being asked to voluntarily quarantine, or even be forcibly quarantined, within the country, Japan extrajudicially denied them landing permission and were returned to the countries from which they came from to get their paperwork in order and try again.

This action made the news as it was unprecendented and historic. Even criminals can reenter Japan (although they will be promptly arrested and put in jail or prison. Albeit a jail or prison that is inside Japan).

The International Answer

The United Nation's Universal Declaration of Human Rights (UDHR), to which Japan is a signatory, answers this clearly in Article 13:

1. Everyone has the right to freedom of movement and residence within the borders of each state.
2. Everyone has the right to leave any country, including his own, and to return to his country.

This makes sense as combined with the United Nation's Convention on the Reduction of Statelessness, the UN's goal is to make sure that everybody has a "home country" they can retreat to in case the place you're living in becomes unlivable, say due to governmental or economic collapse (failed state), war, or pandemic (ex. COVID19).

The Constitutional Answer

The Japanese Constitution does not have a specific article addressing the right for nationals to enter or re-enter Japan. It does have a specific article regarding the right to leave Japan and to also get rid of your Japanese nationality, which conforms to UN Human Rights, according to Article 22, paragraph #2:

• Freedom of all persons to move to a foreign country and to divest themselves of their nationality shall be inviolate.

Paragraph #1 of the same article is often called Japan's "freedom of movement" article in the Constitution:

• Every person shall have freedom to choose and change his residence and to choose his occupation to the extent that it does not interfere with the public welfare.

However, there's a catch: the last thirteen words of that clause.

"to the extent that it does not interfere with the public welfare"

There are many rights in the constitution that are suffixed with the "public welfare" condition. The State of Japan has been loath to ever use the "public welfare" exception with respect to any of the rights it grants to its people, as its meaning is intentionally vague.

Some have argued that in the case of a global pandemic, where the entry of a person who is known to have a deadly and easily contagious disease who almost certainly would spread it to other people in the country even if extraordinary quarantinne measures were taken, the Japanese government could enact the "public welfare" exception to deny Japanese nationals the "freedom to ... change his residence [by returning to Japan]."

The  Immigration and Quarantine Law Answer

The laws below the highest law (the Constitution of Japan), domestic laws, spell out procedures for the return of Japanese nationals in the Immigration and Quarantine Laws. Article 61 of the Immigration Control and Refugee Recognition Act (Immigration Act) stipulates as follows:

"A document is needed certifying that a Japanese person (excluding crew members) returning to Japan from an area outside Japan has a valid passport (if he or she does not have a valid passport, then something else to confirm that he or she has Japanese nationality.") is in their possession. The immigration inspector, through procedures specified by the Ministry of Justice Ordinance, shall receive confirmation of their return from the immigration officer."

In other words, a valid non-expired Japanese passport -- or an equivalent legal document proving identity and/or Japanese nationality, like a valid Japanese driver's license, as this does specify one's 本籍 {honseki} (registered domicle), which proves Japanese nationality -- is needed to return to Japan. Furthermore, immigration authorities can only "confirm" their return to Japan, not "permit" (or not permit). In other words, the Japanese immigration authorities do not have the authority to refuse the return of Japanese people.

However, Article 5 of the Quarantine Law has the following provisions:

"For ships arriving from abroad or aircraft arriving from foreign countries (hereinafter referred to as "ships"), any number of persons must be issued a quarantine certificate or provisional quarantine certificate. Lacking this, they may not land or land objects from the vessel, or leave the location designated by the quarantine station director for each aircraft and quarantine airfield, and they may not carry out objects (hereinafter omitted)."

This article is meant to apply to the captain and crew of cargo and passenger vessels moving freight, but it can in theory apply to anybody. It is believed that this is the "loophole" used to prevent the three Japanese mentioned above from entering Japan.

Why is this a loophole?

Because the law stipulates that it's allowing CIQ (Customs, Immigration, & Quarantinne) to refuse "landing" on the territory of Japan, this means that the Japanese nationals lacking proper COVID19 documentation could have been thought of as not technically "expulsed" or "deported" from the jurisdication of Japan to a foreign country; they never managed to arrive and land and be inside Japan. You can't be "deported" from a place you were never in to begin with!

Legal Japanese nationals have the irrevokable "right of abode" in Japan.

But by being at the Japanese airports CIQ area, weren't these Japanese already "inside" Japan?

Yes.

The State of Japan's jurisdiction, which is an island nation, extends not only to its territory but also to its territorial waters and airspace. When the Japanese arrive at the airport, they are already at least physically within Japan's exclusive jurisdiction. It is in the state of "being".

Not just France, but Russia used the airport
"transit zone is outside jurisdiction" claim to
shield Edward Snowden from the U.S.A.

International law agrees. The French government once claimed that the transit zone at Orly Airport (Aéroport de Paris Orly) was outside the French jurisdiction, but that claim was dismissed by the European Court of Human Rights more than 20 years ago.

The U.S. movie "The Terminal" was partially inspired by the true story of the 18-year stay of Mehran Karimi Nasseri in Terminal 1 of Paris-Charles de Gaulle Airport, from 1988 to 2006.

It's unlikely that same event could occur today due to the latest interpretations of law, which regard airport transit areas as no longer being considered to be legal "territorial jurisdiction limbo zones."

Did the Japanese government make a mistake?

Until these Japanese nationals sue the government (which is a right granted to them by Article 17 of the Constitution), we can't be certain, but many Japanese refugee and immigration issue experts within Japan have opined in the media that inexperienced CIQ officers made an error in interpreting and executing the law.

What should have happened was that these Japanese should have, at the most, been fined for not having proper paperwork and/or voluntarily or if necessary for the "public welfare", forcibly quarantinned within Japan if their health condition warranted such a precaution for the public good, but they should not have been returned to foreign countries if they had made it inside Japan and had proof they were Japanese.

What about non-Japanese with legal Permanent Resident Status or Spouse visas? 

The "right to enter a foreign country" is not recognized by either Japanese or International Law. Even if you have a long term visa or so-called "permanent resident" status.

It's important to understand that even having Permanent Resident Status does not mean you have the "permanent" ability or "right" to be in Japan. You merely have permission, and this permission can be taken away while still be compliant with domestic and international laws (with the exception of stateless people and legally recognized refugees). They can remove your ability to be in Japan based on current laws (ex. commiting a crime), or they can simply make new laws or remove existing ones to take away a non-citizen's right of abode.