Regarding the application for Japanese passports of minors, Japan issues passports by having a signature of a custodian as a legal representative to the application form.

However, if the other parent has expressed his/her disagreement on the issuance of the child's passport to the Japanese Embassies or Consulate Generals beforehand, the passport will usually be issued after the verification of the consent of both parents. In this verification process, the Japanese Embassies and Consulate Generals check with the parent who disagreed beforehand on the issuance of child's passport whether he/she is now willing to submit a "Letter of Consent for an Application of Passport".

In (country, state etc.), the taking a child under (age) abroad without consent of his/her spouse who has custody may be accounted to criminal liability. In fact, there are cases in which taking parent was arrested in charge of child abduction when she reentered a country, or a taking parent was placed on the international wanted list of ICPO. To prevent Japanese citizens from such disadvantages, the Japanese Embassy (the Consulate General) is checking verbally to confirm the existence of agreement of both parents on the application for child's passport, even if there is no declaration of disagreement from one parent. Thank you for your understanding.

http://www.denver.us.emb-japan.go.jp/files/000258330.pdf