Generally Sim free does not mean the same as unlocked. Sim Free just means it has no sim, but it can still be locked to a carrier, so would only support a sim from that carrier.
I do not believe there is any place to buy an outright unlocked iPhone in Japan, and only a few carriers offer unlocking to my knowledge.
https://www.nttdocomo.co.jp/english/support/procedure/simcard/unlock_dcm/
http://www.softbank.jp/en/mobile/support/usim/unlock_procedure/
If there's any place you may be able to get an unlocked iPhone that would be an Apple Store.
You'll need to ask for a specifically unlocked iPhone, to use with any carrier outside of Japan.
Note however, that the warranty will only be valid in Japan, and if you need a service on your iPhone any Apple Stores or Authorized service provides in your country may decline to offer service.