Typical amateur pianists in Tokyo practice piano at home with a digital piano with headphone on weekdays. They reserve a piano studio and go there on weekends.
Here are some piano studios I used to go. You need to call to make a reservation.
Piano Studio Noah http://www.grandpiano.jp/
18 locations across Tokyo.
I used to go to the one in Ikebukuro. There are 14 separate small rooms.
Some of their studios are for non-classical band players.
Go to the website and click the links on the left side for each location. Each page has pictures of the studios.
b-tech Japan http://b-techjapan.com/
Toranomon Station (Tokyo) / Shin Osaka Station (Osaka)
How to book http://b-techjapan.com/studio_tokyo.html
Bösendorfer pianos, large space, good for a group.
If your musical instrument is not too big, then take your violin, cello, clarinet, guitar or whatever it is with you and go to the karaoke place.
Some karaoke places may not like customers playing musical instruments in the ‘box’, but don’t worry, there are so many karaoke places all across Japan. You’ll find the one you can use as your practice room.
Karaoke rooms are great because they have sound insulating doors, ceilings and floors.
One young professional violinist said in an interview that she goes to a karaoke place to practice her violin during her tour in Japan.