Mitsutoki Shigeta, 24, made headlines last year when it emerged he had paid several women in Thailand to have his babies, and was keeping them in a Bangkok apartment.
They were later taken away by Thai authorities as investigations were launched over possible human trafficking violations by Shigeta.
"We can confirm that the courts have given custody of three of the babies to Shigeta," said Pornthep Rasmi, judge and secretary general at the Central Juvenile and Family Court.
"There are no pending cases over the remaining nine children," he said.
Shigeta had earlier said he wanted to produce between 100 and 1,000 babies, according to the co-founder of an organisation that provides surrogacy services in Thailand and other countries.