I believe the IATA database is what the airlines use to determine whether they'll allow someone to fly to a country. You can enter the details of your son's trip into this site and get IATA's opinion:
http://www.iatatravelcentre.com/JP-J...quirements.htm

Even though IATA seems to suggest it will be fine, my advice would be to pay for an expedited passport renewal rather than travelling on a soon to expire passport.

If your son does travel with his current passport, he might find that it's no problem at all, but I would advise him to be prepared for some questions from the immigration officials. It might be a good idea to prepare some documents to back up his story - i,e. print out his itinerary, airplane tickets, insurance documents, hotel reservations and evidence of funds to support himself.