Is there a difference between a Japanese national and citizen?

In some countries, there are multiple tiers of residents. For example, for the United States, there are aliens, permanent residents, nationals, citizens, and natural-born citizens. All U.S. citizens are U.S. nationals, but not all U.S. nationals are U.S. citizens. A person who is from American Samoa, for example, is a U.S. national, but they are not a U.S. citizen; they cannot vote in U.S. national elections or run for national office. People from American Samoa have a U.S. passport, but their passport has a special printed comment on the last annotations page: "THE BEARER IS A UNITED STATES NATIONAL AND NOT A UNITED STATES CITIZEN." For the U.S., both foreign aliens and U.S. passport holding American Samoa, Swains Islands, etc., U.S. nationals may upgrade their status via naturalization (!) to become U.S. citizens. Even so, naturalized Americans are not considered to be "natural-born" and may never be President of the United States. U.S. permanent residency is similar to Japanese permanent residency, in that you can lose it if you're outside the United States for too long and you don't/can't renew your reentry permit. U.S. permanent residency, like U.S. nationality and citizenship, may obligate you to pay U.S. taxes even when living outside the U.S. and/or having abandoned permanent residency depending on your income and asset situation.

India, too, has different tiers of residency: Alien, OCI (Overseas Citizen of India), PIO (Persons of Indian Origin), and Indian citizenship. The "C" in OCI is misleading in that you do not get an Indian passport nor do you get the right to vote or hold office. It is similar to U.S. and Japanese permanent residency except that it's designed primarily for people who live overseas outside of India and never expires. PIO is like "OCI light" in that it expires after 15 (sometimes 20) years.

In Japan, the residents are: aliens, permanent residents, special permanent residents, citizens, and the Imperial Family *. Permanent Residency is basically a residency visa (although it's technically not a visa) with no expiration date or living/work restrictions while in Japan. Special Permanent Residents, due to history, get some extra considerations and treatment similar to citizens: lack of border and alien registration fingerprinting, the ability to go in the Japanese citizen line at immigration, an almost impossible to revoke alien residency status, and a special ID card that is different from and has less information than the new 在留カード {zairyū kādo} (Residence Card): the 特別永住者証明書 {tokubetsu eijūsha shōmeisho} (Special Permanent Resident Certificate) which also contains one's CJK 正字 {seiji} (true/registered sinograph name) in addition to the alphabet passport name.

* The Japanese constitutional monarchy is a special case that's neither a proper subset nor superset of rights compared to other Japanese residents; they have specific Constitutional Articles detailing their status and restrictions and responsibilities. While they are residents and they enjoy extraordinary privileges that neither Japanese citizens nor aliens have, they are also heavily restricted in what they can do, especially with respect to participation in Japan's democracy. For example, they don't have family/last surnames. In fact, they don't have 戸籍 {koseki} (family registers) like Japanese citizens. Additionally, they don't have the right of suffrage, equality under the law, or freedom of matrimony. In a way, they have even less rights/freedoms than alien residents of Japan.

However, once an foreign resident naturalizes to Japanese, they are legally a national and a citizen, and there are no other tiers above them or rights or legal freedoms that a jus sanguinis — by birth (to a Japanese national) — national citizen has that they don't have. A naturalized Japanese national / citizen, for example, can legally become the Prime Minister of Japan.