Traveling with a Japanese and USA passports from and to Japan?

Question:

I've tried finding the answer but all I got was more confused. I've just had my son this past June. He was born in Japan to an American and Japanese parent. He now has dual citizenships with passports. We all live in Japan.

I'm planning to visit the states with my son and wanted to know how I will show his passports to both sides of the countries?

Most searches come up telling me to show Japanese passport when existing & entering Japan. Likewise, show USA passport when entering & existing USA. My question than is this. Won't the Japanese official ask where is my son's chop on his j passport when we enter back to Japan?

Answer:

Airline check-in in Japan
You need to show his U.S. passport and must have booked the flight using his U.S. passport details. The airlines are supposed to report the passport details of their passengers to the U.S. government prior to travel. He could not use the Japanese passport since in this case he would need an online travel authorization (ESTA) to travel under the Visa Waiver Program.

Japanese exit immigration inspection
You present his Japanese passport to the Japanese authorities when you leave the country.

U.S. entry immigration inspection
You present his American passport; should you be asked why it has no visa stamps entered you show the Japanese passport and state that your son has dual citizenship,

Airline check-in in the U.S.
You can show either passport since both authorize the travel to Japan; the Japanese based on Japanese citizenship, the American based on the visa exemption agreement on reciprocity.

U.S. exit immigration inspection
Is not performed.

Japanese entry immigration inspection
You show his Japanese passport; should you be asked why it has no visa stamps entered you show his U.S. passport and state that your son has dual citizenship.

Japan does not allow dual citizenship. It is only tolerated if it has been acquired at birth. Your son has to decide which citizenship to finally keep before he turns 22 years..

@yopparaiiii:
To answer based on your additional details:
There is no need to conceal the U.S. [dual] citizenship to Japanese authorities since it has been acquired "involuntarily" at birth, hence tolerated in Japan. You have gotten bad advice at your Embassy.

@ RealAnswers:
U.S. law demands U.S. citizen to enter/leave the U.S. using a passport/travel document issued by the United States [legal basis: section 215 of the U.S Immigration and Nationality Act (8 U.S.C. 1185)]. An ESTA application would be refused.