As discussed many times on this blog, Japan uses Sony's FeliCa standard for mobile payments, such as Suica, Waon, Edy, etc. Quoting Eido Inoue:
FeliCa is Sony developed "Japanese NFC" and is much older than the international NFC system that was inspired by it. Early Japanese phones (smartphone and feature phones) were FeliCa only; newer (all 2014 models and most 2013 models) Japanese market Android docomo phones with NFC are hybrid NFC+FeliCa. Non-Japanese phones are NFC only.The tech specs so far only list NFC as included on the iPhone 6. Perhaps you recall the debacle surrounding the advertising for the LTE iPad, which misled many non-US consumers to think it was compatible with their local 4G networks. This time around, the marketing department at Apple has done a much better job. There is simply no mention of "Apple Pay" at all on the Japanese website.