The Japan Aerospace Exploration Agency (JAXA) has a main facility in Tsukuba, about 1 hour by train from Tokyo. There is an excellent exhibition space full of satellites and other space tech. The best part is the free entrance and guided tours for only ¥500.
The GoodThe Not-So Good
Free space exhibitionNothing much else nearby
Guided tour of functioning facility

Tsukuba is a city north of Tokyo about 1 hour by train from Akihabara or Asakusa station. You then take a bus from the bus terminal outside the station direct to the Space Center. There are a ton of bus routes that go clsoe to the space center so you will just have to figure it out yourself once at the bus terminal. Worse case you can walk there in 40 minutes. There are other ways to get there from Tokyo but the direct train from Akihabara is the most tourist friendly. If you have the JR pass then use the Joban Line to Arakawaoki Station and get a bus from there.

Rocket displayed outside the Space Center – image from Wikipedia

There is detailed information on the English section of the Jaxa website including how to book guided tours in English. The Space Dome is the main exhibition area and is free to enter, with plenty to see. JAXA has a number of facilities throughout Japan, many of which are open to visitors.

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