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The body scanners at Narita and other Japanese airports appear to be Millimetre wave scanners. The purpose is not to detect things under the skin such as an implant, but things between the skin and the clothing. In short, these, and the similar x-ray type of scanner, basically can see under clothing.
Millimetre wave scanners are known to have a relatively high false positive rate. In particular, it seems that folds of clothing or multiple layers of clothing might make it appear that there's "something" underneath your clothing that needs checking.
Also, a lot of scanners now run software that automatically flags up areas of concern (e.g. check this person's right arm), rather than displaying the full image, because of the obvious privacy concerns.