Rehearsal studios for 'studio live' in Tokyo
Sound Studio DOM, Koenji
Events are regularly held at this very punk studio, usually in their larger room, but also in their smaller ones. They also have a rooftop area where you can drink and have barbecues. You basically pay the hourly rental price plus 900 yen for staff.
Studio Zot, Asagaya
Rinky Dink Studios
This rehearsal studio chain allows studio live events in some of their locations. You'll need to call them for details.
Some of this chain's studios have rooms set up for gigs.
They have a live spaces called Attack (48) and Music Inn 50 respectively, although at about 7000 to 8000 yen an hour, it doesn't end up much cheaper than booking an actual live house.
These spaces are more reasonable than the Shinjuku and Akihabara ones, at about 4000 to 5000 yen an hour.
Maldic Studio, Kita-Sando
This place which is not far from Yoyogi station allows live events in one of its studios for around 3000 yen an hour.
Bass on Top, Nakano
Gateway Studio, Shibuya
At 6000 yen an hour including 2 staff members to help with the PA, you can organise gigs here.
Little Monster, Shinjuku-Gyoen
This place has very reasonable prices (15000 to 19000 total) for mini live shows.
Studio Bayd, Shimokitazawa
This place seems to work somewhat like a live house.
A lot of other rehearsal studios with a big enough room will allow studio live events. Just discuss it with them. Here are a few that have allowed live events before:
Studio Revole, Akihabara
Studio UEN, Nishi-Ogikubo
Studio PACKS, Kita-Senju
Studio Koyaama, Koenji
Hill Valley Studio, Shinjuku
Studio NODE, Shinjuku
Noah Sound Studio, various locations