There is great misunderstanding about the ability of a parent outside Japan to obtain access to a child in Japan through the Hague Abduction Convention.
The Hague Convention contains only one provision (Article 21) concerning visitation. That Article states little more than that an application to make arrangements for organizing or securing rights of access may be presented to the Central Authorities of Contracting States.
Japan's statute implementing the Convention into Japanese law states that an application may be filed under the Convention for visitation only (a) with respect to a child who is located in Japan, (b) who was, immediately before the visitation became unable to be made, a habitual resident of another Hague country, (c) by a person who is entitled to such visitation under the laws of said state other than Japan.
Essentially what all of this means is that no Hague Convention access application can be made in Japan if the child is habitually resident in Japan at the time the alleged right of access has been violated.
This is confirmed by the Japanese Ministry of Foreign Affairs' own explanation of the visitation provisions of the Convention. This states that an access claim in Japan should be dismissed unless the applicant is entitled to visitation or contact with the child under the laws of the state where the child held his or her habitual residence immediately before the visitation could not be made.
This means that whenever a child is taken to Japan and becomes habitually resident there within the meaning of Japanese law, no access claim can be made under the Hague Convention.
The parent outside Japan will then have no right to see the child except by bringing a regular custody case in a Family Court in Japan and must expect that, even if such a claim is ultimately successful , it will (a) almost certainly be limited to visitation in Japan itself (visitation outside Japan has never been ordered by a Japanese court, to my knowledge), (b) will probably be limited to a few hours a month, (c) will be probably be strictly supervised in a courthouse or other specific location, and (d) will most likely be unenforceable in Japan.
If a child living outside Japan is lawfully relocated to Japan (whether by court order or parental agreement) the habitual residence of the child will shift to Japan relative quickly after the relocation.
At that point it will be unclear whether the parent outside Japan “is entitled” to visitation under the law of Japan. If there is not even a foreign court order requiring such access there will be no such right in existence. If there was a prior foreign order that purported to make provision for such access, the parent living outside Japan will be entitled to commence a court proceeding in the Family Court in Japan to ask the court to recognize and enforce the foreign custody order. However, the other parent in Japan will be entitled to ask the Japanese court to assume full custody jurisdiction, since the child will be habitually resident there, and to issue a new custody order that would exclude any provision for contact by the other parent. Alternatively, the parent in Japan will be able to start a new custody case in Japan at any time after the child is settled in Japan and to ask the court there to give unlimited sole custody to such parent.
Accordingly, any expectation that Japan's accession to the Hague Convention allows parents outside Japan to secure access to their children lawfully living in Japan is quite mistaken.