The foreign ministry said it intervened in a case involving a five-year-old boy, brought to Japan by his Japanese mother, who left the boy's German father.
The mother took the boy in June without the father's consent, a ministry official said.
"In August, the father contacted us to request assistance. We have located the boy, and contacted the mother," he said.
"In October, the mother took the boy to his home," he said, adding that the parents will have to work out their difference in Germany.
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Japan had long been the only member of the Group of Seven major industrialised nations not to ratify the convention, which requires nations to return snatched children to the countries where they usually reside.
Japanese courts virtually never grant custody to foreign parents, which has previously left few legal avenues for those whose former partners have fled to Japan with their children.
Hundreds of US parents have complained that they have been left unable to see their half-Japanese children. At least 120 have filed cases in Japan, invariably to no avail.
The Japanese government has 13 pending requests from non-Japanese parents for return of their offsprings taken to Japan, the foreign ministry official said.
There are nine cases where Japanese parents are asking for return of their children taken abroad, he said.
The foreign ministry has also accepted 46 requests from non-Japanese parents requesting meetings with their children in Japan but not asking for their return.
There are 13 cases of Japanese parents requesting meetings with their kids taken abroad, the official added.