- BOAT by Voyage Ventures 

http://voyage-ventures.com/english

- NEW'S BASE by NOMAD 

http://newsbase.in/pc/

- Lightningspot 

http://lightningspot.com/

- HUB Tokyo 

http://hubtokyo.com/

- 01 Booster 

http://01booster.com/

- Open Network Space 

http://space.onlab.jp/pricing.html

- Samurai Startup Island Samurai Startup Island

http://www.samurai-startupisland.asia/

- co-ba 

http://tsukuruba.com/co-ba/

- The Terminal 

http://theterminal.jp/index.htm

- Portal Point 

http://portalpoint.jp/

- Academy Hills 

http://www.academyhills.com/

- Kurkku Home 

http://www.kurkku-home.jp/

- Creative Lounge MOV 

http://www.shibuyamov.com/en/

- Mina no Shigotoba 

http://hatchcowork.com/space/coworking-2/

- Arinko 

http://www.ants-office.com/

- Ths Scape(r) 

http://www.thescape-r.jp/

- Sakura Works 

http://sakuraworks.org/

- MassxMass 

http://massmass.jp/shareoffice

- Tamariba 

http://tamariba.me/

- Harajuku Terrace 

http://harajukuterrace.com/

- Check out this google map for Incubation facilities and co-working spaces for tech startups in Tokyo

https://maps.google.com/maps/ms?gl=us&ie=UTF8&oe=UTF8&msa=0&msid=215693144356033562781.0004af6900612a8869e94&dg=feature