Originally Posted by
kansaiflyer
The gist of that page, from the US Customs and Border Patrol Agency is this: In a true emergency, when a US dual national cannot obtain an American passport, they can travel to/from the US with their second passport. Here is the relevant passage: "If you have a true emergency, and are unable to obtain a U.S. Passport before your travels and have only a VWP-eligible country's passport, then you will have to file with ESTA to use that passport to travel to the U.S., and you will have to use the non-resident queue when arriving at the U.S. airport using the foreign passport."
Was it a true emergency that prevented you from postponing your flights (the fact that this may cost several thousand dollars doesn't make it a true emergency in all cases) in order to obtain a US passport for your son before departing Japan?
Did you have to deal with a true emergency for the entire duration of your time in the US and return to one in Japan such that you were unable to obtain a US passport before departing, and also couldn't postpone your return until you could obtain one? (While a US passport is not usually checked by a human when leaving the US to a country of which one is a citizen, this is not relevant)