Japan has a parliamentary government with a constitutional monarchy, for its leadership. The capital is located in Tokyo. Similer to the US they have 3 branches, Judicial, Legislative, and Executive.
Tokyo individually is run by their Metropolitan government. Most major cities have them. There are 47 in total. The Tokyo Metropolitan Government is the government of the Tokyo Metropolis, one of the 47 prefectures of Japan. The head of the government is the senator, while there is an elected assembly. This government is just for Tokyo, not all of Japan. These govenments reign under the main government located in Tokyo. Japan is a very structured place.
I got these pictures from Culture Grams