Now you can use Apple Pay in Japan. See below link.
Use Suica or PASMO cards on iPhone or Apple Watch in Japan

Apple Pay was started October 26 in Japan.
Apple started Apple Pay in October 2014 at United States. Many Japanese iPhone user were waiting from that day to pay by Apple Pay in Japan. In japan, mobile payment is very popular payment way. Because many Japanese mobile phone (such as Feature Phone and Android) were support mobile payment system a long time ago.

Major mobile payment system in Japan is Suica, iD, QUICPay, Rakuten-Edy, nanaco and waon. Apple Pay is support Suica, iD and QUICPay (Yes, Japan’s Apple Pay is based on the Japan mobile payment system. Not only that, also support infrastructure by Apple Pay system.). Suica is not only payment system. It is the most popular transit card distributed by JR East in Japan east erea.

But it is not perfect in Japan’s Apple Pay. Global Apple Pay system is NFC Type A or B. But in Japan’s Apple Pay is NFC Type F. iPhone 7 japan model is support only NFC Type F. And global model is only support Type A and B.
So if you trip to Japan, you can’t use Apple Pay in your iPhone. I think it is very crazy and nonsense. But may be future iPhone will support NFC Type A/B/F. In japan’s smart phone are already installed NFC Type A/B/F. So I think future iPhone will also install NFC Type A/B/F too.

Be careful your iPhone can’t use Apple Pay in Japan this day. You must need credit card or cash exchanged in japan payment now.