It is common for English-language news reports to use a country’s capital to refer to the government of that country. For example, “Washington” refers to the government of the United States, and “Beijing” refers to the government of China. However, when Japanese-language news reports refer to Tokyo, they are referring to the city of Tokyo, not the government of Japan.
Instead, Japanese reporters use the word “Nagata-cho” to refer to Japanese national politics, as this is the name of the area of Tokyo where the the Japanese parliament is located. However, despite the fact that the Prime Minister’s Official Residence (首相官邸, Shusho Kantei) is in Nagato-cho as well, the term specifically refers to parliament, not the prime minister. Likewise, “Kasumigaseki” is the name of the area where most of the ministries are located, and it is used when people want to refer to the Japanese bureaucracy. However, the people who use these phrases are mostly MPs and journalists; ordinary citizens don’t usually use the words in this way.
In the US, there is a similar phenomenon. Journalists use the phrase “Capitol Hill” to refer to Congress, as this is the area of Washington where Congress is located. But they say “White House” to refer to the president. They use the phrase “Foggy Bottom” to refer to the US State Department, since Foggy Bottom is the neighborhood of Washington where the State Department is located.