A minor child between foreign parents with different nationality is most likely to have a dual nationality (nationality of mother and father). The governing of the law of the custody upon the divorce or separation is a critical issue if the governing law of the father and mother is different. 

In practice, the laws of Japan shall be the governing law of the parental authority and custody right of the miner child upon the divorce or separation of the foreigners in Japan as long as the child was born and grew up in Japan.

Please see more details below.

international-divorce-between-foreigners_parental-authority-and-custodial-right