We are residing in Japan but is it OK to leave Japan and visit the Philippines for an emergency reason on Aug. 19, 2013 if my son's U.S. passport will expire on Sept. 16, 2013?
It is against the regulations which ask for 6 month validity but allow discretion for validity down to 60 days. Since the passport in question expires less than 30 after your arrival, entry will most likely be refused.
For emergency reasons, your consulate may provide service to renew the passport faster than the usual delay. I would call them immediately and prepare proof of the said emergency.