Japan is often described using both broad regions, such as Kanto or Tohoku, and its 47 prefectures.
These are not the same kind of division.
Prefectures are official administrative units. Each has its own governor and government. Japan has 47 prefectural-level divisions: Tokyo, Hokkaido, Kyoto and Osaka, and 43 prefectures.
In Japanese, their official endings are different: Tokyo is a to, Hokkaido is a dō, Kyoto and Osaka are fu, and the others are ken. In everyday English, however, all 47 are usually called prefectures.
Tokyo can feel like a world of its own because of its enormous population and urban scale. Administratively, though, it still occupies the same prefectural level as Hokkaido, Osaka, Aichi, or any other prefecture.
Below the prefectures are cities, wards, towns, and villages. In Japanese, addresses move from larger areas to smaller ones, as in:
Aichi Prefecture, Nagoya City.
Regions are different. Kanto, Chugoku, Tohoku, and the other regions are broad groupings of several prefectures.
They are useful when talking about where something is located or when describing wider cultural areas. Japan is commonly divided into Hokkaido, Tohoku, Kanto, Chubu, Kinki or Kansai, Chugoku, Shikoku, and Kyushu.
These regional boundaries are not always as fixed as prefectural borders. Okinawa may be included with Kyushu or treated as a separate region. Chubu may also be divided into smaller areas such as Hokuriku, Koshinetsu, and Tokai.
The unit Japanese people use to describe where they live often depends on who they are speaking to.
When talking to someone from another part of Japan, saying “I live in Aichi Prefecture” is often enough. When speaking to another person from Aichi, it is more natural to say “Nagoya City” or even name the ward, because that gives a clearer sense of the actual local area.
Saying “I live in the Chubu region” gives only a rough location. It is too broad to function as an address.
Regional names are also used in expressions such as “Kansai people” or “people from Tohoku.” In this case, the name is not about administration. It refers more loosely to shared speech patterns, food, local character, and regional images.
The simplest way to understand the system is this:
A region is a broad way of looking at Japan geographically or culturally. A prefecture is an official unit used for government and addresses.
Kanto or Kansai tells you the general part of Japan and may suggest a cultural area. Tokyo, Osaka, or Aichi tells you a more specific place.
Regions and prefectures are not competing systems. They are two different ways of looking at the same country, at different scales.