Cash is king. To the point where many vending machines will take 10000yen (~$100) bills and return a stack of 1000yen (~$10) bills plus some coins when you buy a drink (however, most drink machines won't take anything bigger than 1000yen).
RFID cash replacement cards exist (as do ways of using your mobile phone as one), but places that accept them are rare outside the vicinity of train stations (or even in, in western Japan).
EFTPOS seems to be rarer that the RFID readers.
You can make online puchases with some places (eg, Amazon), and pay in cash at the local Lawson convenience store. COD is very common. Lawson even has a system where you can book for certain popular places (tokyo dysney, ghibli museum, etc) and pay in-store. Paying for your mobile phone is the same: many convenience stores will do the processing for you. Seems to be free, too (probably built into the mobile billing system).
The most technologically advanced country on the planet still likes to rub two coins together.