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The "new" listings for the categories I monitor all seem very commercial- therefore likely paid inclusion, or very non-commercial- therefore likely to be freely included.
Yahoo!Japan does not review any commercial sites from free submission
We have tried submissions as well as asked them directly and it is no go. If you want to be in you have to pay.
The other problem is that if you do not have sufficient Japanese content they will reject the paid listing. You then have to go through the appeal process once you have added "sufficient" Japanese content.